This will help you greatly.... CLICKY: TrePaul's Auto to manual swap
It cover's my friend's swap on his '01 4x4 that I was deeply deeply involved in. TONS of info to be found between the conversations and the problems and whatnot. Including a complete parts list.
A couple of things to consider....wiring was a bear and I honestly cannot help you there....it's been like 3+ years. Confusing the computer to think it's in neutral until a manual PCM was installed. PCM either needs replaced with a manual then VIN changed, or your existing changed to a manual....this will eliminate the issues of the 3,000rpm limit.