I think you will find the Transmission are the weakest link in the drivetrain. You can drastically improve them with some minor modifications.
There are quite a few guys making over 500 rwhp with littel more than new rod bolts.
I'm pretty sure the biggest differences between 99 - 02 are the PCM's and programming.
I don't really know anything about nitrous, but there are people here who can help.
Welcome aboard.
No more trucks, but this is what I used to have. 2000 GMC Sierra, 6.0L-LQ4, Built 4L60, LS6 Cam, The Other Guys Headers, 3 inch exhaust and 7 chamber flowmaster, 43lb injectors, Nelson Tuning, Drop - 3/4 McGaughys Spindles, Bell Tech Shackles & Hangers. Best time 13.59 @ 106