I would say screw a stock shifter, the stock ones are junk, and an aftermarket floor shifter is so much easier. If looks matter, get a shifter that looks like a 4 speed shifter.
You'll need a rad with a tranny cooler, or a large external cooler. Lines will also be needed. You can use rubber, but it has to be the right fittings and right rubber. They are rather expensive, so steel PITA lines will probably be your choice.
Your 4 speed should be held in by two arms that hold it up from the sides, kinda like motor mounts, when the auto will have a cross member that it'll rest on.
I say rip the pilot bearing out with the fly wheel, no need for it anymore.
I'm pretty sure you'll need a new starter, automatic style.
A patch of sorts for the tranny hump will be needed... onless you need a place to tos your beer when the cops pulll you over.