Extremely Odd Electrical Issues - Car is Completely Dead
9/1/20, 11:53 PM
#1
Extremely Odd Electrical Issues - Car is Completely Dead
This is going to be a long one as it's got a lot of layers and I don't want to leave out any detail that may turn out to be important.
2006 Mustang GT, low boost single turbo setup, just dyno'd 500hp a few months ago. 40k miles on the car.
This started when I forgot to put my battery tender on the car after driving it and when I tried to start it the battery was completely dead. Pushed the car out of the garage so I had room to work, tried to charge the battery but it wouldn't take a charge. Odd thing I noticed is when the charger was connected there was a weird humming noise coming from the back of the car. At the time I thought it was from the rear speakers. It got louder with more amperage from the charger. Pulled the battery, put in another battery. Car fired right up and drove it around the block before pulling it in the garage. Put the battery tender back on it.
Now the problems start:
I try to start it a week later and the battery is completely dead (just a single click and nothing more). Remember the battery tender is connected. So I test the tender, it's working. I put a charger on the car and it takes a charge no problem. Wait for it to charge overnight. Try to start the car and I get a single click and everything goes dark (interior lights shut off, gauges shut off, etc.). Acts like a bad battery connection. Dig into that, find one battery connection a little loose, tighten it down, try again. Same thing, just a click and it all goes dead.
So I test the battery thinking it must be dead, it's got full voltage. Unhook battery, clean connections (even though they were clean), reconnect everything. Open the door and it's got power to the car again (lights come on inside). Turn the key and it starts making a weird clicking noise (relay noise) from the passenger side under the dash, gauge cluster is dimly flashing, and there is a hum from the rear of the car that matches the pattern of the relay clicking on/off.
So I turn off the ignition, get out of the car and notice the tail lights are dimly flashing at the same rate as the noise that's coming from the passenger side rear fender area. Try to lock the doors and they lock but then won't unlock. Use key to unlock door. Try to roll window up as it's halfway down from going down 1/4" every time I've opened the door. Windows won't work. Interior map lights won't turn on. Radio is dead, headlights are dead, gauge cluster is dead, power seats are dead, everything is dead other than the random relay and electrical noises. Unhook battery and all noises stop. Connect battery and noises return (no key in ignition). At one point a loud clicking noise under the hood turned out to be the throttle body fluttering.
Here is a video of it making noise as soon as I connect the battery. Tail lights are flashing at the same pulse rate as the hum you'll hear:
Throttle body fluttering. I don't even remember what combination of things I did before it started doing this as this was a month ago and it hasn't don't it since:
Here's what it does when I turn the key on/off, try to lock/unlock the doors, a quick look at the tail lights flashing, etc:
I tried to scan codes but since the car has no power (or intermittent power for only a split second at a time when the relay clicks) it won't connect to pull codes.
I tried pulling one fuse or relay at a time in the under hood fuse panel to see what would stop the noise. No relays changed anything when unplugged. Fuses 62 and 63 made the noise from the rear passenger side of the car stop when unplugged. Disconnecting fuses 46, 56, or 59 made new noises appear, always a rapid on/off noise from different components. No other fuses had any effect on anything.
At first I thought maybe the PATS stuff got triggered by all the dead battery problems but it's certainly more than that at this point (though I'm not ruling it out as one of many problems).
My best guess is that one of the many body modules somehow go screwed up and it's killing power to the rest of the car. Problem is, I don't know where all of these modules are, or how to test any of them as I don't have a dealer service manual for that sort of thing.
If anyone knows of a download link for the dealer service manual(s) for this car, I'd love to have it.
I've currently got a car I can't use, can't sell (for any decent value), and it's way too nice of a car to just rot away in the garage. It's already been like this for 3 months. I feel like this is the sort of thing that if I send it to the dealer (something I've never done in my entire life as I've always worked on my own cars), they'll spend a whole bunch of time (and my money) trying to figure it out and not ever figure it out since it's such a weird deal. Only chance at a dealer would be to find a really knowledgeable tech and that's difficult to come by.
I don't even know where to start with diagnosing this problem so I'm hoping someone has had something similar happen (though I doubt I'll be that lucky).
Any help would be greatly appreciated
2006 Mustang GT, low boost single turbo setup, just dyno'd 500hp a few months ago. 40k miles on the car.
This started when I forgot to put my battery tender on the car after driving it and when I tried to start it the battery was completely dead. Pushed the car out of the garage so I had room to work, tried to charge the battery but it wouldn't take a charge. Odd thing I noticed is when the charger was connected there was a weird humming noise coming from the back of the car. At the time I thought it was from the rear speakers. It got louder with more amperage from the charger. Pulled the battery, put in another battery. Car fired right up and drove it around the block before pulling it in the garage. Put the battery tender back on it.
Now the problems start:
I try to start it a week later and the battery is completely dead (just a single click and nothing more). Remember the battery tender is connected. So I test the tender, it's working. I put a charger on the car and it takes a charge no problem. Wait for it to charge overnight. Try to start the car and I get a single click and everything goes dark (interior lights shut off, gauges shut off, etc.). Acts like a bad battery connection. Dig into that, find one battery connection a little loose, tighten it down, try again. Same thing, just a click and it all goes dead.
So I test the battery thinking it must be dead, it's got full voltage. Unhook battery, clean connections (even though they were clean), reconnect everything. Open the door and it's got power to the car again (lights come on inside). Turn the key and it starts making a weird clicking noise (relay noise) from the passenger side under the dash, gauge cluster is dimly flashing, and there is a hum from the rear of the car that matches the pattern of the relay clicking on/off.
So I turn off the ignition, get out of the car and notice the tail lights are dimly flashing at the same rate as the noise that's coming from the passenger side rear fender area. Try to lock the doors and they lock but then won't unlock. Use key to unlock door. Try to roll window up as it's halfway down from going down 1/4" every time I've opened the door. Windows won't work. Interior map lights won't turn on. Radio is dead, headlights are dead, gauge cluster is dead, power seats are dead, everything is dead other than the random relay and electrical noises. Unhook battery and all noises stop. Connect battery and noises return (no key in ignition). At one point a loud clicking noise under the hood turned out to be the throttle body fluttering.
Here is a video of it making noise as soon as I connect the battery. Tail lights are flashing at the same pulse rate as the hum you'll hear:
Throttle body fluttering. I don't even remember what combination of things I did before it started doing this as this was a month ago and it hasn't don't it since:
Here's what it does when I turn the key on/off, try to lock/unlock the doors, a quick look at the tail lights flashing, etc:
I tried to scan codes but since the car has no power (or intermittent power for only a split second at a time when the relay clicks) it won't connect to pull codes.
I tried pulling one fuse or relay at a time in the under hood fuse panel to see what would stop the noise. No relays changed anything when unplugged. Fuses 62 and 63 made the noise from the rear passenger side of the car stop when unplugged. Disconnecting fuses 46, 56, or 59 made new noises appear, always a rapid on/off noise from different components. No other fuses had any effect on anything.
At first I thought maybe the PATS stuff got triggered by all the dead battery problems but it's certainly more than that at this point (though I'm not ruling it out as one of many problems).
My best guess is that one of the many body modules somehow go screwed up and it's killing power to the rest of the car. Problem is, I don't know where all of these modules are, or how to test any of them as I don't have a dealer service manual for that sort of thing.
If anyone knows of a download link for the dealer service manual(s) for this car, I'd love to have it.
I've currently got a car I can't use, can't sell (for any decent value), and it's way too nice of a car to just rot away in the garage. It's already been like this for 3 months. I feel like this is the sort of thing that if I send it to the dealer (something I've never done in my entire life as I've always worked on my own cars), they'll spend a whole bunch of time (and my money) trying to figure it out and not ever figure it out since it's such a weird deal. Only chance at a dealer would be to find a really knowledgeable tech and that's difficult to come by.
I don't even know where to start with diagnosing this problem so I'm hoping someone has had something similar happen (though I doubt I'll be that lucky).
Any help would be greatly appreciated
9/2/20, 08:17 AM
#2
Tms Mustang Member ------ The Customizer!
Here's the online service manual.
http://iihs.net/fsm/?d=1
I've had many electrical issues with my car but nothing this severe. If I think of anything I'll post it. Good luck.
http://iihs.net/fsm/?d=1
I've had many electrical issues with my car but nothing this severe. If I think of anything I'll post it. Good luck.
9/2/20, 09:35 AM
#3
Legacy TMS Member
Just taking a guess at the weird hum... you got a Shaker 1000? That'd explain the right rear quarter panel humming. Amps are goin' nuts, those speakers are having a lot of fun. 
My guess at what this is is the Smart Junction Box is fried. For whatever reason. May be just corrosion from the famed passenger side water leak issue, or just lucky. But everything going on screams SJB. It's located where the inside fuses are, and is in fact where those inside fuses live. Right kick panel. Here's a video I found to show you where it is. Can't speak of quality or work safe language or such, just it shows where it is:
I'm sure I could find a better one... But it also talks about the water thing. Thing is that a 'new' SJB may need programming unless you get the exact replacement for the exact body configuration of your car... and even then. There's stories both ways, 'I got it and plugged it in, tada!' and 'I got it and plugged it in, but things wouldn't work, hadda get it programmed.' So be aware of that.
Past that...
http://iihs.net/fsm/?d=40&f=Componen...on%20Views.pdf
Major components, besides the SJB and the BEC (engine fuse panel) to maybe disconnect and see what happens:
Engine Computer/PCM. Right front engine bay, three connectors, 'blade' looking thing. Right side of the radiator is *right* in front of it. Lever off the connectors, pretty easy. There's a fourth connector on the side, do that one too. Check car. 'Fixed' inside? There's your problem, bad PCM/harness at PCM. Be aware that the weather seals may move around on disconnect, and can cause your car to have a real fun time when the connectors don't quite connect right... https://themustangsource.com/forums/...4/#post7051179
Main interior harness connector, left firewall, under brake booster. Disconnect, check for corrosion. I might save that one last though, it'd be a pretty weird failure.
Instrument cluster. Remove bezel, remove instrument panel.
If you wind up taking out all of these, and the car's still broken, you are definitely going to have to go through it with a fine toothed comb nearly wire by wire with a multimeter and some test pins/probes.
Of course, I'd do all the disconnecting, reconnecting with the battery off, just to be sure things didn't get really strange. 'Bout all I got... Hope that helps. Good luck!
My guess at what this is is the Smart Junction Box is fried. For whatever reason. May be just corrosion from the famed passenger side water leak issue, or just lucky. But everything going on screams SJB. It's located where the inside fuses are, and is in fact where those inside fuses live. Right kick panel. Here's a video I found to show you where it is. Can't speak of quality or work safe language or such, just it shows where it is:
I'm sure I could find a better one... But it also talks about the water thing. Thing is that a 'new' SJB may need programming unless you get the exact replacement for the exact body configuration of your car... and even then. There's stories both ways, 'I got it and plugged it in, tada!' and 'I got it and plugged it in, but things wouldn't work, hadda get it programmed.' So be aware of that.
Past that...
http://iihs.net/fsm/?d=40&f=Componen...on%20Views.pdf
Major components, besides the SJB and the BEC (engine fuse panel) to maybe disconnect and see what happens:
Engine Computer/PCM. Right front engine bay, three connectors, 'blade' looking thing. Right side of the radiator is *right* in front of it. Lever off the connectors, pretty easy. There's a fourth connector on the side, do that one too. Check car. 'Fixed' inside? There's your problem, bad PCM/harness at PCM. Be aware that the weather seals may move around on disconnect, and can cause your car to have a real fun time when the connectors don't quite connect right... https://themustangsource.com/forums/...4/#post7051179
Main interior harness connector, left firewall, under brake booster. Disconnect, check for corrosion. I might save that one last though, it'd be a pretty weird failure.
Instrument cluster. Remove bezel, remove instrument panel.
If you wind up taking out all of these, and the car's still broken, you are definitely going to have to go through it with a fine toothed comb nearly wire by wire with a multimeter and some test pins/probes.
Of course, I'd do all the disconnecting, reconnecting with the battery off, just to be sure things didn't get really strange. 'Bout all I got... Hope that helps. Good luck!
9/2/20, 02:27 PM
#4
Here's the online service manual.
http://iihs.net/fsm/?d=1
I've had many electrical issues with my car but nothing this severe. If I think of anything I'll post it. Good luck.
http://iihs.net/fsm/?d=1
I've had many electrical issues with my car but nothing this severe. If I think of anything I'll post it. Good luck.
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VGMStudios (9/3/20)
9/2/20, 02:28 PM
#5
Just taking a guess at the weird hum... you got a Shaker 1000? That'd explain the right rear quarter panel humming. Amps are goin' nuts, those speakers are having a lot of fun.
My guess at what this is is the Smart Junction Box is fried. For whatever reason. May be just corrosion from the famed passenger side water leak issue, or just lucky. But everything going on screams SJB. It's located where the inside fuses are, and is in fact where those inside fuses live. Right kick panel. Here's a video I found to show you where it is. Can't speak of quality or work safe language or such, just it shows where it is:
https://www.youtube.com/watch?v=vasJ_HGv9mY
I'm sure I could find a better one... But it also talks about the water thing. Thing is that a 'new' SJB may need programming unless you get the exact replacement for the exact body configuration of your car... and even then. There's stories both ways, 'I got it and plugged it in, tada!' and 'I got it and plugged it in, but things wouldn't work, hadda get it programmed.' So be aware of that.
Past that...
http://iihs.net/fsm/?d=40&f=Componen...on%20Views.pdf
Major components, besides the SJB and the BEC (engine fuse panel) to maybe disconnect and see what happens:
Engine Computer/PCM. Right front engine bay, three connectors, 'blade' looking thing. Right side of the radiator is *right* in front of it. Lever off the connectors, pretty easy. There's a fourth connector on the side, do that one too. Check car. 'Fixed' inside? There's your problem, bad PCM/harness at PCM. Be aware that the weather seals may move around on disconnect, and can cause your car to have a real fun time when the connectors don't quite connect right... https://themustangsource.com/forums/...4/#post7051179
Main interior harness connector, left firewall, under brake booster. Disconnect, check for corrosion. I might save that one last though, it'd be a pretty weird failure.
Instrument cluster. Remove bezel, remove instrument panel.
If you wind up taking out all of these, and the car's still broken, you are definitely going to have to go through it with a fine toothed comb nearly wire by wire with a multimeter and some test pins/probes.
Of course, I'd do all the disconnecting, reconnecting with the battery off, just to be sure things didn't get really strange. 'Bout all I got... Hope that helps. Good luck!
My guess at what this is is the Smart Junction Box is fried. For whatever reason. May be just corrosion from the famed passenger side water leak issue, or just lucky. But everything going on screams SJB. It's located where the inside fuses are, and is in fact where those inside fuses live. Right kick panel. Here's a video I found to show you where it is. Can't speak of quality or work safe language or such, just it shows where it is:
https://www.youtube.com/watch?v=vasJ_HGv9mY
I'm sure I could find a better one... But it also talks about the water thing. Thing is that a 'new' SJB may need programming unless you get the exact replacement for the exact body configuration of your car... and even then. There's stories both ways, 'I got it and plugged it in, tada!' and 'I got it and plugged it in, but things wouldn't work, hadda get it programmed.' So be aware of that.
Past that...
http://iihs.net/fsm/?d=40&f=Componen...on%20Views.pdf
Major components, besides the SJB and the BEC (engine fuse panel) to maybe disconnect and see what happens:
Engine Computer/PCM. Right front engine bay, three connectors, 'blade' looking thing. Right side of the radiator is *right* in front of it. Lever off the connectors, pretty easy. There's a fourth connector on the side, do that one too. Check car. 'Fixed' inside? There's your problem, bad PCM/harness at PCM. Be aware that the weather seals may move around on disconnect, and can cause your car to have a real fun time when the connectors don't quite connect right... https://themustangsource.com/forums/...4/#post7051179
Main interior harness connector, left firewall, under brake booster. Disconnect, check for corrosion. I might save that one last though, it'd be a pretty weird failure.
Instrument cluster. Remove bezel, remove instrument panel.
If you wind up taking out all of these, and the car's still broken, you are definitely going to have to go through it with a fine toothed comb nearly wire by wire with a multimeter and some test pins/probes.
Of course, I'd do all the disconnecting, reconnecting with the battery off, just to be sure things didn't get really strange. 'Bout all I got... Hope that helps. Good luck!
Thanks for all of this info. I'll dig into it (and the links) hopefully tonight when I've got some time.
9/2/20, 05:37 PM
#6
Legacy TMS Member
No shaker, eh? Huh. Well, then, I'm not terribly sure what's comin' from that right rear now... 
Can't recall anything else. There's the door lock on the door, tensioner of the seat belt, shaker subs if you have 'em, the fuel level sender on that side and... that's it. 
On a coupe, anyway. Convertible, there's motors involved too for the top and the quarter window, but you got a coupe, so not applicable... No way it's just the right side modded tail light... is it?
http://iihs.net/fsm/?d=40&f=Componen...Views.pdf&p=15
Very strange. Lookin' forward to knowin' what happened there...
Can't recall anything else. There's the door lock on the door, tensioner of the seat belt, shaker subs if you have 'em, the fuel level sender on that side and... that's it. On a coupe, anyway. Convertible, there's motors involved too for the top and the quarter window, but you got a coupe, so not applicable... No way it's just the right side modded tail light... is it?http://iihs.net/fsm/?d=40&f=Componen...Views.pdf&p=15
Very strange. Lookin' forward to knowin' what happened there...
Last edited by houtex; 9/2/20 at 05:39 PM.
9/3/20, 01:05 PM
#7
Tms Mustang Member ------ The Customizer!
I didnt see the videos until now.
Two things I would try.
Unplug your taill ights then plug the battery in, see if the noise is still there.
Disconnect the SJB and open it up and look for corrosion. Mine had some because of the water leak. Cleaned it up and fixed a broken pin. Works fine now.
Two things I would try.
Unplug your taill ights then plug the battery in, see if the noise is still there.
Disconnect the SJB and open it up and look for corrosion. Mine had some because of the water leak. Cleaned it up and fixed a broken pin. Works fine now.
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