Thanks for the responses.
The shifting problem started suddenly after about 2 years of flawless operation. I can think of nothing that would have caused this - I was putting around trying to adjust a new carburetor, then realized that it wouldn't shift up without some serious force. Based on this, I know that the problem wasn't due to something being installed improperly - so I know that that is out of the way.
Yes, this is my first time opening a 250R case (it's an '88 by the way). I have built car engines, etc, but never opened a 250R case. All of the testing instructions sound a bit confusing, but as I reassemble, I will keep these instructions in mind and hopefully be able to give it a test as Jerry indicated.
Clutch: the clutch seems to be about halfway through it's life (it's a Henson Billet Proof). There are very minimal notches in the basket from the plates - I have heard many people mention to file them a bit - I will do this before re-installing it. Beyond that, it would roll forward with the clutch was engaged, but only after it warmed a bit - while cold, it would actually stall by engaging 1st gear which the clutch pulled in and at idle. While warm however, it was fine. I assumed that this was a typical 250R characteristic and it had never caused my any issue before - it is worth mentioning however.
So I will go ahead and start reassembly soon. Lets say I have about $500 more in the budget to spend on the engine - which transmission components should I go ahead and replace in hopes that I find the "bad" item? Has anyone heard any feedback on the billet steel forks on eBay? I'm afraid to buy OEM, used ones, because they may be more worn than mine.
Thanks guys.