Well the issue wasn't the pressure plate being installed backwards to the torque converter. There has been a few cases (based on factory techs) that have seen them installed facing the wrong way and making a noise.
Oh well, back to the exhaust system since the drive train has been taking apart twice with no luck in solving the issue.
The really depressing news now is two new '04s on the lot make the same exact noise. My dealer is still trying to solve it, because he believes it is BS that the cars make that god awful noise. But he says he has only 2 ideas left and then it might require an after market fix. Which means maybe going to an X crossover pipe instead of the stock H.