Approach the bottom end in a way that all bases are covered and you might as well do any upgrades that you may need now since you're going in there.
Here's a quick list:
-kicker idler bushing
-modded shift shaft, shift star, roller detent arm
-pancake bearing
-fresh clutch and replace any worn components
-fresh seals and good sealer (don't forget to put sealer on the keyway on the crank'a primary gear)
-crank trued and welded as well as fresh outer bearings if it's in good shape
-transmission bearings
-replace any misc. clips, retainers, and use full clips where you can (get it from a vendor here and not the dealership)
Also, if you are ever considering a much higher output motor in the future, consider doing the trans while it's out of there. There are guys that can do some machining that helps it shift a bit more like a honda instead of a Mack truck.