Re: discoloration near drain hole
Hope this isn't too late...
I experienced the same thing around the splashwell drain. Dug out a cavity of rotten wood about half the thickness of the transom, about maybe five, six inches across, roughly circular area. On advice of the guys at West Marine, I filled it in with 3m High Strength Marine Filler - it's a 2-part putty. Fiberglassed over it.
I didn't treat it with anything to kill the rot though. That was three years ago...I am convinced I removed all the soft wood, but I don't know if rot has continued to spread, although I haven't seen any evidence of it. Since then, the most convincing article I've read about stopping rot advised applying anti-freeze to the area and drying it out before filling.
Sorry don't still have the link - they tested various products and got better results than with bleach or some other commercial rot killing products. I know that glycol is a killer, not sure why it would be better than bleach but then I'm no chemist.
good luck...