For engine drivability problems, any dealer, and maybe most other shops, will always want to go back to stock as a baseline. Therefore I would remove the TH fix and see if that changes anything. The air filter is not stock and that could be another problem. I guess I'm just saying to be prepared for a diagnosis along that line. People don't like to hear that sort of diagnosis but the fact is that engine mods change performance characteristics, sometimes for the better and sometimes not. At the least you might have to expect to take some bad with the good. As for the noises underneath, you may be right but the only sure way to find out is to get the car up in the air and take a look. Let us know what the outcome is.
Karl
