The shifter bushing was still intact, although I have a new marlin one waiting to go in. The shift pattern isn't sloppy at all. Good suggestion though, I'll change it before dropping the tranny just to be sure that's not 3rd gear problem.
Pinion bearing... you mean the pilot bearing? I'm pretty sure that's not it because the noise can be duplicated with the clutch engaged. Same reason rules out the throwout bearing.
I'm definitely going to scrutinize the 3rd gear synchro, gear, and corresponding teeth on the counter gear once it's apart.
Fresh marlin tranny does sound nice, but it's not in the budget at this point. I'd like to learn more about it anyway because the transmission is the only part of these trucks I haven't worked on yet. I think I would understand and respect the transmission a lot more if I did it myself. If a full rebuild is where this heads, don't worry. Marlin is the only source I trust for the rebuild kit.