Mike, Ref #'s are Clymer M447-2 (kx500 '83 -'02)
I had a similar problem with shift/hang-up with mine.
Ended up being a shift fork was bent (spread open too far #63 pg 284 distance between tip of b and tip of a) and "ends" were worn pretty good [#65 pg 284].
The Shifter pawl was bent [#8 pg255] and the shift shaft was also [#7 pg 281].
I had to replace all three. When I say bent it was not like a 45 or anything, it was just a few degrees.
Roll the shift fork shaft on a piece of glass or granite etc. with a lamp or flashlight behind it. look for light underneath or use a feeler gauge to probe along it (like a spatula).
As you roll the shaft watch the ends and middle closely to lift off the surface.
The shift pawl was "opened up", as was the shift fork, and I couldn't figure out how to close-up the inside dimension of either one and still keep them straight
so I replaced them.
The shift forks are stamped if I recall "L" & "R", [front,left and right is determined by the position of the rider on the bike. pg4 fig 4]
The other thing I started doing was test fitting the cases,tranny crank and all before final (sealant) assembly. It is a pain, however it payed off in the long run.
That's an XR story for another day
Had to buy new case gaskets...(plural..
) and watch out for thin washers sticking to the case halfs and then falling out of place (trans shafts).
There's another thread about inaccuracy in the Clymer, no ones perfect I guess, It has been great for me, I didn't have the sheckles for the FSM. But will try to get one!
Please Note: It sounds like you know what you're doing, so don't take this all wrong. It's just what happened to me.
Tuck\o/