Lot's of threads on pulling the prop on here. First hint: Leave the prop nut on a few threads; you don't want the prop popping loose and clanging on the ground (or your toe). I got a two-jaw gear puller from Harbor Freight (make sure it's big enough), tightened it down, then whacked on the end of it which popped it loose. Others have used a 2x4 and a big hammer to whack on the back side of the prop. Or, you can beg, borrow, or steal a real prop puller.
You'll have to remove the coupler from the transmission end also. You're gonna have the same kind of problem - simply removing the nut that holds the coupler on won't release the propshaft. People have had good success with similar approaches as the propshaft - or you can drill four holes in a piece of steel plate, put four bolts through and screw them into the coupler, and tighten them down to put force on the propshaft to push it out of the coupler. Once you have the coupler removed, the propshaft will slide right out the back of the boat - no need to lubricate the strut bearing in this situation. If you do want to lubricate, use water (or the "personal lubricant" of your choice) - petroleum based lubes may destroy the rubber inside the bearing.
Now let's talk about that shaft log. If you've worn through the side of it, you're going to leak water into the boat. That's generally a bad thing, especially since the shaft log represents a fairly big hole in the bottom of the boat. I've never done anything to mine, so I'm not an expert here, but I think this is something you need to fix. I don't know if this is reparable or needs to be replaced.
You'll need to figure out if your strut is bent. Disconnect the coupler, and see if the strut is pointing the propshaft through the shaft log without touching the sides. It's possible that the engine/transmission were so far out of alignment that they pushed the shaft against the side of the log, or it's possible that the strut got bent and it's the thing pushing the shaft against the side of the log. Figure out which it is. If it's the strut, search here for "bent strut" for suggestions on repairing or replacing. If the propshaft slides through the strut and goes through the shaft log easily, then it was an engine alignment issue that you're going to fix anyway.
But with that amount of misalignment, I'd seriously consider changing the cutlass bearings while you're at it. The all-plastic "Vesconite" bearings have had good reviews.
1998 Maristar 200VRS