I have a 1994 xt 600e. The chassis number is JYA3WRT08NA****** and the motor is a 3AJ. The clutch cable is on the left hand side of the engine. Since rebuilding the engine and gearbox I have had a lot of trouble with the clutch. When the engine was cold the bike would change gear smoothly and neutral is was easy to find. When it got hot the clutch wouldn't clear and dragged. You could feel the bike creeping along even when the clutch was pulled in. Neutral was impossible to select and gear changing was rough.The hotter it got the worse it got. I tried EVERYTHING to sort this out. New cable, different oils, endless adjustment of the cables and rod inside the engine. I even sent the whole clutch assembly to a specialist who builds clutches for drag bikes and he said it was all good. By this time I had pulled the right hand casing on and off five times and was ready to sell or burn the bike!!
I mentioned this problem to an old british bike mechanic who did some machining work for me and he reckoned it was the clutch friction plates. His theory being that if the plates were old and had been run in lots of different types/grades of oil they could get sticky when hot even though they looked ok. So, I roughed up the metal clutch plates with 80 grit emery paper, fitted some genuine Yamaha friction plates and a new actuating rod (the one that runs through the middle of the motor. The spiral ends were scuffed and worn) and now the clutch is now perfect, no drag, no sticking, smooth gear changes and neutral is easy to get even when the motor is good and hot.
I would also like to recommend Loctite 518 as an engine gasket sealant. I have been using it for years and it is just brilliant for stopping leaks.