looking at doing a Gen3 swap ???

1) does the factory harness come equiped with all the connections for the auto trans and manual trans?
2) In all the vehicles that come with either trans as a option. that way you can swap from one or the other and the PCM do what its suppose to do.
3) also are the PCM's same for either trans or you have to get one that goes with that trans.

When I do this swap I think I will find me a good used truck to strip down, this would be the cheapest route to get all the parts needed.