I have been reading this thread with interest, I too have been having the with 2nd gear in my TR250. It isn't a grind it is like hitting a wall, won't go into gear. I rebuilt the tranny myself, all new synchronizers, bearings and bushings,most of the time it shifts perfectly, but sometimes I have this issue, the other day I thought maybe it was occuring when the tranny/car had been running a while and got hot, but it did it from cold the other day. Topped up the gear oil, no difference, I have tried pumping the clutch, then shifting, doesn't help, it does seem to be happening less since I put a return spring on my clutch pedal but still occurs.
If it was mechanical in the gearbox don't think it would come and go like that, it it was hydraulic I would think pumping the clutch would make a difference.
I am stumped, I also tested clutch arm travel roughly .6" give or take which seemed in the ballpark.