OK ... lots 'o questions; which is a good thing.
Phil does sell the rubber used to plug that screw hole; I learned it the hard way in reusing a screw without the lead washer; bad mistake. I caught mine, however, with oil shooting out everywhere; before I put the tub back on. Live and learn. Don't forget to tap the center plate securely in that area after placing the plug in; that center plate needs to sit flush to the power unit. That's where that little screw is very important; it also pulled the center plate down to the power unit making a good seal and without it, you will have to make sure that plate is all the way down to the power unit.
You are probably OK with the alignment of your tub to the center plate, Larry. Keep it at a quarter of inch if that's what the book says. It is apparent that the water got in from the center plate not being sufficiently water tight. Those bolts with the rubber washers are very, very important.
You can probably reuse what you have but order a couple more from Phil ... the short ones ... for the middle of the center plate. You tighten it down but don't over-tighten. Just take it to the point on the socket wrench where it's getting harder to tighten; don't crank on it.
Did you get the water out of the right angle drive? Probably going to be OK.
Could the leak from the seal by the flywheel have been caused by the water mixing with the oil? Those transmissions were not designed to hold water; only thick lubrication. Was it just a few drops or LOTS of oil dripping out? I've noticed that on my pink E, it has had water in the transmission, and that area leaked drops of black lubrication out; not a lot but enough to PO me! When the transmission fluid got changed, the leak stopped.
If you're uncomfortable with your original power unit, keep using this one. Clean it up (don't use hot water this time ... OK? ... only parts cleaner), re-gasket and try again.
I hope I'm helping you with my advice, Larry. I don't want you to have the Valdez in your basement shooting out Bosco!!
Wish I had a video tape or something to show you how to do this but I think you're going to get it. Just don't get PO'd; go slow ... you're very mechanically inclined.