I suspect that your problem may go away if you swap in a known good VB. Right now between the VB being wrong(and who knows what the previous person did to it), the part throttle kickdown stuff, the shift kit, and grinding, bending, adjusting this and that there are too many things that could be wrong. I would try a different valve body in it and if it works then put the transgo stuff in it.

In theory, there is no difference between theory and practice. In practice, there is.