M50D-R1 is the manual trans of choice.
This is about all that should be new but, the Flywheel should be in good condition. Either new, turned for a fresh surface, or in a very good condition.
Hardest part for myself was the actual install of the trans to get the first couple bolts stabbed. Then the wiring was the next hard part. This all depends on how far you want to go with it. Do you want it to work like it was stock, or just working? ie...reverse lights, no cel light, no start in gear, etc...
You will drain the fluids upon removal, and will never get all the fluids out of the trans unless you tear it down pc by pc. So being stored with some fluids in it, is just fine. You can store the trans upright standing on the bell housing.
Thanks gman! Now I saw the list that foxracin has put out of the parts needed, I think its pretty complete, what is a floor plate? Is there an exploded view of the transmission and its parts etc somewhere on here? Where can I find a factory shop manual, I am sure that would have what pictures I am looking for. I need a specific view of all the trans and clutch stuff to kind of have a better idea of what I'm looking to be doing.