Hey there,
Have you tried adusting the clutch cable/pedal freeplay to make sure the clutch is disengaging from the engine fully? The cables do stretch/come out of adjustment over time, especially if you got a new one when you did the clutch/rebuilt the engine. I've had an '88 Samurai and a '90 Tracker that would both start doing that same thing when the clutch was coming out of adjustment. They would both get to that "borderline" area where sometimes it would shift fine, other times it would grind/not go into gear. My Tracker nearly stranded me in a mall paking lot one day when it came so far out that I couldn't get it into gear at all without turning off the engine. Luckily, I had my tool set in the truck, adjusted it right there in the parking lot, and was on my way again.