I have a 05 4.0 mustang the battery was replaced2 month's ago and alternator today. When i jumped the car too start it and everything ran fine until i took the jumpers off and it died . the windows a/c and radio where cutting on and off on the way home before the alternator swap . i have issues with water getting in from the passenger side cabin air filter leaking water on the harness and a small electronic box . im clueless on what is causing the power failure. Also im on my way too have the new alternator tested just too make sure its not a bad apple thanks for any help .

 

If water is getting inside the car.. It's almost 100% likely to be your smart junction box that's causing your issues.. Have it checked as soon as possible !

 

Agreed - smart junction box.

 

Thirded... Less than smart Smart Junction Box goin' on here.

 

The engine dying when you remove the cables is a sign of the alternator not working. If the car starts and runs with cables attached it should run with them off. Granted the sjb can be an issue with some of your symptoms but it doesn't know when you are removing the jumper cables and making it die. The engine management is run by a different module. Yes the modules have to communicate with each other but if the car is running with jumpers attached it should run with them off.

 

After having read the OP's post that mentions having issues with water getting in from the passenger side cabin filter leaking water onto the harness and then traveling down towards the location of the SJB.. It would pretty much indicate that it's the SJB as the likely culprit.. However his car also shouldn't die the moment the battery cables are removed following jump starting either.. Therefore I agree that it appears he also ended up getting a defective alternator as well

 

Isn't the water leak cause from the water drains under the cowl getting clogged with debris? I seem to recall this problem, where the passenger side carpet got wet.