Ford Repair: Unknown Noise from Transmission, mach 1 mustang, transmission area

Question
I have a 2003 Mach 1 Mustang. I am hearing a grinding noise that seems to be coming from the transmission area when the transmission is winding down, either while shifting or slowing down . I can't really tell where the noise is coming from. The noise is not really noticeable until the car warms up (it gets noticeably louder once the car is warm). I took my car in to the dealership and they told me that nothing was wrong with it, and that the noise was there before and is louder now due to my new exhaust system (Full Bassani: headers to cat-back). Got any other ideas of what could be causing it? If so, I'll take my car to another dealership and have them look at it.

Answer
Jeremy-

  Without knowing where the noise is coming from it's hard to pin specifically what could be causing it.  My guess is that something in the drivetrain has loosened itself up and it knocking, but that's just a guess.  I can tell you that, unless it's a motor issue, your exhaust is not the culprit of "making it more noticeable" (Bassanni...nice choice by the way...sounds soooo nice).  I'd certainly get a second opinion on that or try and pin down the area where it's coming from.  

Steve