It doesn't matter what was done to the mufflers, if you have OEM headers, which it sounds like you do, then it is still going to act like a stock system. The headers are the restricting part of the system, anything done downstream of them will have very little, if any, impact.
Try returning to an OEM set-up, jets-#152.5, #90, #170, oem needles and springs.....remove airbox tape, etc. and see what that does for you.
Try returning to an OEM set-up, jets-#152.5, #90, #170, oem needles and springs.....remove airbox tape, etc. and see what that does for you.