I've noticed on my trans with maximized valve body pressure, and one extra clutch disc per pack, that under slow (coasting or light braking to a stop light) decelerating in 3rd or 2nd, it will bang pretty hard on the down shift when in Drive. I've determined this is due to the shift not having the proper rpms (higher). If I just slow down a bit quicker, more braking, it's always very crisp. Acceleration is always perfect for the upshifts It can just catch you off guard sometimes. But in general, a modified trans just seems to be a bit more particular about shift points, but it's easy to manage in Tip mode.

Get that thing on a dyno and make sure it's all buttoned up. Sounds like it's always been tuned on the aggressive side. Water meth could help that.