4L80E swap isn't working correctly...need help.

My buddy and I swapped a 4L80E into a 99 Silverado(NBS). We got the pins in the right slots(22 and 23) and bought Nelson's adapter kit. But the truck won't run correctly. Before the speed sensor wires were hooked to the ECM, it ran like it should, it just wouldn't shift correctly. After connected pin 22/23, it won't take WOT. It kinda just makes a lot of noise or just bogs down like the pedal isn't being pressed. We are sure the truck had plenty of gas, fluids were fresh and topped off. No vacuum leaks.
Here's what it does. He takes off from a stop - full throttle, won't break the tires loose(No TM) and barely moves the truck. Max speed with pedal floored was around 60 or so and took a long time to get there. The trucks would sound very rough and out of tune. But when he uses part throttle, the truck hauls ass like it should and the trans will shift like it should and the truck sounds smoother aswell. Another thing we noticed is that it's moving in neutral and reverse doesn't seem to work...as if it's locked or fighting a forward gear....the truck will rock backwards then jump forward.
I realize the Neutral and reverse problems could be linkage related, but that doesn't explain why WOT doesn't work. I'd appreciate any ideas or advice.

did you have your pcm reflashed to control the 80? i had experience with a camaro that did the 80 swap and had to have a new OS installed to operate the 80.

Yes, Nelson retuned for the 80.

Most autos will move (drive) in N when cold 'cause the fluid is cold and "sticky". Can't help with the rest right now.

Be sure the vss is setup correctly, meaning, the rear vss is the original vss, meaning it should be on the tailshaft.
The two wires you mentioned are for the front vss, the ISS, this is the speed sensor near the middle of the case, those two wires go there and to the pcm.
The original vss, the rear one, the output vss, goes to the pcm as well, but you shouldn't have mess/moved with that one, it stays in it's original connector pins.

What gear does the trans start off in when you put the truck in Drive, if it's slow, probably second gear.

let me know,
allen

The cats could not have plugged up could they? Unplug what you plugged in that started the issue and see if things return to how they were before.