833 4spd repair advice

I use ATF fluid in all mine. Not gear oil. Shifts fine not a problem.
If he ran it for a short time without lube it could have caused some damage. Are the counter shafts bearings or just bushings? (thinking out loud) Fill it to the bottom of the fill plug with ATF and run it to see if it quiets down, drain it warm and fill it again. You might be able to save it with minimal damage.
I took the pin out after I set all the linkages yes. When I was just running the shifter through all the gears without engine running, first and second were real short and 3rd and fourth were longer and smoother, but overall, I was surprised at how 'rough' it shifted with it being freshly rebuilt. But figured it may be because there was no fluid or something, I wasn't sure.