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.