There are 3 main possiblilities:
1)- mis-adjusted shifter linkage (the adjustment procedure in the Owners Manual work well if followed exactly.)
2)- not enough disengagement of the clutch- check this by fully depressing the clutch & shoving a flat-blade feeler gauge down thru the bellhousing access hole, between the flywheel & clutch disc. If you cannot get an 0.030" blade in there, yoiu have a slave or master cylinder problem. Master dylinders internally bypass pressure with no external leak so this can be tricky to find. I've also seen bad-outa-the-box replacement parts, so don't overlook your new long-throw slave as a possible contributor
3)- due to being driven a long time with problem #1 and/or #2, the ZF synchronizer is too badly worn to function. A complete tear-down & replacement of the steel synchro and the mating gear cone is the only option. This can cost upwards of $2500 and no other source of genuine ZF parts can be found anywhere except from RBT Transmissions in So-Cal.