I share Manny and blackmercedes opinion based upon my experience with old school carb'd motors (larger diameter exhaust reduced initial backpressure and provided more noise but yielded lower low-end performance/torque)
Perhaps trans or driveline is slipping? Other things to take a look at: accel linkage/ potentometer, bowden, trans/ trans modulator, leak down and compression test
Do you have before and after dyno with/ without the new exhaust? Any software upgrades in the works?
Let us know what it turns out to be