Roush Lost torque w/x-pipe?

bummer about the loss of seat of the pants torque after the x-pipe install. You are not the first guy I have heard that from. I should know. I did the same on my 02 S281 n/a. I had the Borla set up from Saleen (they went to the magnaflow in 03) I felt a little less torque also after installing the "real" bassani x-pipe.
The only thing I could tell you would go with 3.73's and get Saleen to re-flash for that. That is probably the cheapest way to go to get back the feel you had and keep the insane sounding improvement with the new pipe. You know they do advance the timing in the powerflash. I had to have mine done over after I picked up the car because I actually had some detonation. Out on the west coast we only get 91 octane from the pump so we have to deal with that for the most part.
Good luck.