I also think that the low-end torque is due to the ShoShop Y-pipe. My car made ALOT of torque for a mildly modded SVT, but low HP readings with just a SHO-Shop Ypipe. After swapping to the MSDS Ypipe, I noticed a very big increase in top end...but have no Dyno runs to back it up.
I think that the lack of a bend in the SHo-Shop actually HURTS top end...