Take it back to the dealership and have them figure it out. I would request that they take off the CAI and return it to stock.

 

I'm putting my money on the water leak.

 

Man, I would of called a different tow truck company

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I would definetly let the Ford Dealer that you bought it from fix what ever is wrong but I would keep the CAI; it does not sound like that is a problem. The most obvious thing is to lose that wrecker companies phone number.

 

+1 on the water leak, it comes in around the fuse box area and it certainly sounds like you are having some weird electrical issues

 

This is why I would NEVER purchase a used 2005 - 2008 Mustang without first taking it to car wash and running it through 4-5 times. Of course, I do not know of a dealer who would let you do that. I hope that Ford fixes the water leak with the redesign coming in '09 or 10.

 

Damn dude, I amsorry to hear that.
If the car drove fine with the intake before the washing then the intake is not the issue, I am betting on a water leak.

 

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Could have been out of gas...or had bad fuel pressure...

 

Here's what the dealer will say- "Oh, you put 93 octane gas in it? It hates expensive gas!"

Sorry, but I'm on a Breaking Away theme tonight!

Just be glad you bought a certified used car!