On the
service manual, there's online copies of the actual Honda
service manual. For any critical details, I'd reference that manual to be the most accurate. The other branded mauals should be good for general how to's. You can always print the info you need from the digital copy and not care about getting the paper dirty etc.
http://www.oscarmayer.net/atc/manuals/
I'd guess the transmission is alright, but water in the crank area is bad even short term. I'm with yaegerb, split the cases, and bare min replace the crank bearings, seals, and a rod big end bearing. New rod would never hurt too since it's taken down that far. Splitting the case can be kind of scary, but just follow the
service manual and things generally end up fine. If not, post here and we can help with what's missing, what order things should be in etc which is also shown in the manual. I've split a couple of TRX250X engines, it's not that bad when gravity holds everything together and you're just taking one case half off.
Once you get the cylinder and such in the mail, I suspect you'd want to measure it and see if it's standard bore or over sized and buy a new piston/rings to match it, maybe have the cylinder bored if it's standard bore but out of spec, etc. I'm not all that experienced in that area, I just know the piston determines the bore size (always buy the piston first, then have the bore job done to match it). Maybe the piston you have is re-usable, probably depends if it's scored and such.
Anyway, good luck on your build.