1. it's alot easier to mess with that stuff when the floor is off. put the shaft somewhere safe, cover the threads on your water intake so you don't drip resin on them (what a pain in the butt), check the mounting plates for the strut, skegs, and rudder. some people replace these, mine were ok...or so i thought...more on that in #3...
2. depends on whether the coupler wants to come off easily, you can go either way with it when the engine is out. i had to take my shaft and coupler to the prop shop to get them separated.
3. my rudder has a zerk but i've been having problems with water coming in. i wish i had dealt with it when the floor and gas tank weren't in the way.
4. get crafty with reference points. once everything is taken out, it's easy to forget exactly where you are and where things went. don't grind everything completely away until you're ready....the lip of old floor around the hull keeps a reference for floor height, you can mark the hull with spray paint or whatever and grind it away later, cut sections of stringer or engine supports out in large sections so you can use them later for reference...whatever you have to do. templates are good as long as you know exactly where they go.
5. the old rivet holes will get used again. i wouldn't do anything with them unless they're messed up and you can't re-use them. i just drilled new holes for the rub rail. you'll be using sealant for that step so you shouldn't have to bother with sealing the old holes.

read up...rickr also has some great photos and descriptions of his comp rebuild. there are more around here...