Transmission problem
1987 Jeep YJ 6 cyl Four Wheel Drive Manual 150k miles

I initially stared having an issue with shifting a month ago it was somtimes hard to get into 1st and griding reverse.. it got worse to the point I stared checking out the problem. hydraulic clutch fluid was low so i filled it and it was fine. then it kept draining and in turn i wouldnt be able to get into gear... I realized then the slave cylinder was leaking. so i had it replaced and the hydraulic master cylinder replaced... I also had a clutch kit put in(it was needed) the flywheel turned and a new starter ring put on flywheel.... then I get it back from shop and I immediatly have trouble with getting the tranny into gears intermittently(meaning it works OK 10% of the time) and grinds reverse to the point i cannot get it into gear.. when jeep is off shifts into any gear without a problem. I checked hydraulic fluid and it is full. i can sometimes go into 1st from a stop easily and every third time it wont work. if im upshifting to second from 1st i have to go to third gear because it wont go into second. I dont know where to go from here. any ideas what to do first? then if it doesnt work what next and so on.....? if u need any other info i will supply it