Here is my take on your pilot bushing question. You have a fresh cut on the flywheel, new clutch, pressure plate and throw out bearing, but you are going to leave the old pilot bushing in place because it sort of looks ok? Don't do that. You have gone this far, go a little further. They are easy to remove, easy to install a new one, and then all your work is new and fresh parts.
To remove, forget packing the hole with bread or grease and trying to hydraulic it out. Instead, use a 5/8 NC tap. It will thread in, bottom out, and then the old bearing will walk out as you keep turning. Once its out, use some brake cleaner or solvent to clean the cavity all out. Next, I dont know the type of bushing you have, but make sure its bronze and preferably made of oil lite material. Do not grease this bushing, oil maybe, but no grease. You will seal up the pores and the oil in the oil lite bushing will not leach out and do its job. Oil the OD of the bushing and use either a spare trans input shaft or a real install tool, lol, to install it.
For the trans, dont forget to make up a pair of install studs. Cut the heads of a pair of bolts that have a sufficient amount of unthreaded shank so that you can install the headless bolts. Grind a taper on the shank end to aid in starting the trans on the bolts. Then slide the trans in on the shanks instead of running the risk of damaging the input shaft by having too much weight on it while installing it free hand.
