If you gutted the pipes completely you lost too much back pressure thus losing the bottom end torque. There is a reducer up near where the pipes attach to the headers you need to leave in to keep the low end torque. You can put an after market baffle in the header pipe to fix it. Not sure how well it will work but the easiest fix I can think of except another set of pipes.
Available
Here among other places. There is also a selection of other baffles you may want to try in the pipes.
