One way to remove the old pilot bushing is to pack it with grease and then use a dowel rod of the same diameter as the transmission input shaft and a hammer to force it out hydraulically. When it comes out, wipe off the grease (wheel bearing grease is good to use) and drive in the new one using a piece of wood of the same overall diameter and the hammer.
Jon
I've read that silicone caulk can be used and is less messy and less likely to splatter.
I agree that it makes sense to install a new pilot bushing and throw out bearing when the transmission is out for service. The clutch pack would depend on age and performance. Resurfacing the flywheel should be considered.
