If this has been asked before I'm sorry and an admin can delete. Anyway I bought a really run down CT2 a couple of years ago and it had sat in the elements for lord knows how long. My question is.....do you guys ever flush out the clutch/gear box area? If so what do you use.

Unless its full of water in there with the oil i'd just simply get it nice & hot [if its a runner] & go for a ride then change it while hot so everything is held in suspension as much as possible. If what comes out looks real bad just change it again after another longer ride. Don't use a thick oil but use a light grade for the two changes, then go to a standard recommended grade. Sorry i'm just pulling ideas out of nowhere but its probably what i'd do in your situation. If the clutch is toast then it will smell of burnt clutch, but is she grips & drives without slipping it'll be good.
Just to add, if it has got water in there i'd still do the same re changing & flushing so long as it sounds good & not like rusty bearings.