First off, give us a little more info....was this a Magnaflow catback? If so, was it made for the V6 or was it a GT catback that you are connecting to your modified or aftermarket H-pipe.
Also, you didn't lose any torque, it just moved up in the powerband. Even though you don't have as much torque down low, you definitely gained HP up high. When I had my V6 and put on a 2.5 catback dual exhaust, I saw the same thing. Lost the torque down low but got a lot up high. The best way to fix that is to get a set of 3.73's or 4.10's.