Surging and touchy fuel pedal with new FU2 chip

[Huckleberry]

Just finished installing a new FU2 module. I have a surge even with the modified stock setting and it is doing it in all settings 1-6. The pedal has a slight dead spot off idle and then the truck launches forward. I also have a lot of black smoke on hard acceleration (3/4 throttle). My 6 positions are:

modified stock
heavy tow
standard tow
light tow
80 daily driver
whisper

The truck has just went through a heads up overhaul that includes the following:
H11 studs, Comp Cams springs, Smith Bros. pushrods, FF 250/100 injectors, regulated return fuel system, Stealth SRP1 HPOP, HPOP crossover hose, larger turbo, 4" exhaust. The EBPV has been deleted.

I have only driven it 11 miles. I have access to a scan tool. I am getting an IAH heater code (my truck is an early 99, but I installed a later PMT1 PCM). The early 99's did not have an IAH. I also have a PO238 Turbo boost sensor A circuit high and a PO478 exhaust pressure control valve high.

My IPR oil pressure at idle is around 500 give or take 25 psi. I also noticed the idle switch does not show "off" until .82 volts with normal foot off pedal of .59 volts. Could this be the touchy pedal problem?

Thanks for any help