I was wondering if there are any issues I should look out for if I disconnect the battery from the car to install power to the radio or some tail light mods or whatever reason.

I've never had an alarm on a car before, so i don't know if disconnecting power is going to cause issues with the alarm.

 

Just disconnect the negative terminal on the battery and you will be fine. The alarm will not go off or anything like that. I have the factory alarm and have disconnected my battery several times now.

 

Here is what happened to me when I disconnected my battery on my new 06 GT. I picked up the car last week and immediately bought a drop in K@N. I disconnected the battery and installed the filter. When I reconnected it went into panic mode with horn honking and lights flashing. I had to disconnect the battery to stop it. I tried everything I could think of and called the dealer. The service guy told me it had gone into "valet mode" somehow. There is a small button swithch next to the hood release. He had me to reconnect battery which put it in panic mode again, then push and hold in the button while starting the car (prior to this it wouldn't start), let it run for one minute, shut off, get out of the car and lock manually with the key then unlock and open the door. This worked. Has anyone else ever heard of this happening? A friend of mine installed a K@N and had no problem after he disconnected the battery.

 

i did not even know there is was a button there? gonna have to check that out...

 

Why did you have to disconnect your battery to install the filter?

 

I've never done it before just to add an air filter but my understanding is that with the new computer it is good to do so to adjust for additional air. Disconnecting the battery causes it to reset. I noticed that the K&N website now advises to do so.

 

I justlooked on mine, and I think thats the fuel cutoff reset switch, or at least thats what it says below the little reb button

 

I was wondering the same...
I didn't disconnect the battery when I Installed my K&N drop-in, there was no messing around with any electrical part.

 

The 'valet switch' you are referring to is NOT part of the factory-installed Active Anti Theft system. It is typically part of the Ford Accessory Alarm system or an aftermarket alarm system the dealer may have installed.

This also explains why your alarm went off when disconnecting and reconnecting the battery. The factory-installed system would not behave like that.