Hello,
As you and Dave and I know, unless something mechanically changed in the engine, there is no reason to alter the eprom. I am assuming this is a 3 port regulator? The fuel pressure in your application should ramp up from ~13psi stock to ~25psi at WOT at your boost level.

Based on experience I suspect your "new" injectors. I have seen many replacement tbi injectors work fine at stock fuel pressure and fail horribly under higher pressure(stick closed) The fact that your fuel pressure is 40psi kinda tells us that you have no fuel flow unless there is a problem with the regulator(doubtful).

The 99 ecu cannot control the trans except for TCC lockup. The xdf must be improperly labeled. I believe GM called them 4L60 when they went to electronically controlled lockup torque convertor instead of 700r4.