Hi Grandpa, congrats on the Prelude. Sounds like that tranny was in bad shape. I used to be (and still am) a Chevy guy, but I don't mind helping out a Ford guy.

These cars are actually pretty easy to work on once you figure out what all you have to remove in order to get to what you want to work on.
3rd gen preludes don't use pilot bearings. So you can stop looking, lol. The clutch kit should contain the disk, pressure plate, throw-out bearing, and clutch alignment tool.
This kind of threw me too when I did my first clutch replacement. Good luck with the lude, and post some pics of it. We love to look at pictures here.
BTW, what did the new transmission come out of? Easiest would be either from an 88 or 89. If it's from a 90 or 91 you'll need to order a clutch kit for that and not an 88. The transmission splines are different and the flywheel is bigger, so you'll also need the flywheel from the donor car if it was a 90/91.