ok, so i did my intro post already, time to start asking questions , please bear with me, this is a kinda complicated problem

from a 92' YJ with a 4.0 off a i think 89 or so-ish cherokee (XJ?) replaced from a 4.0 from the YJ, engines should be identical
127k miles on chassis, not sure on transmission (has the liquid gasket thing by the rear of the transmssion, not sure if it has been rebuilt or not before) dad just replaced clutch and internal slave

so problem is, when the transmssion is cold, no problems, shifts fine to any gear, except reverse, grinds like crazy, clutch all the way down, and sounds like synco's not working at all

so after maybe 15 minutes or so driving on freeway, not sure on city, i'm sure maybe 20 minutes in city or so, but yea, from a stop, its hard to get into any gear, try and force the lever in, but gears do not engage, pump the clutch, nothing happens but some grinds, from a slight roll, say 2-3 mph, 1st slides right in

bled the hydraulic system, seems to be no air (ran the system dry like twice, kept bleeding it, and eventually no air)

ran the wrong gear lube at least once, tried redline's mt-90, found out it was a gl-4 oil not gl-5, then ran gm syncomesh, that didnt help, no label saying what weight and grade oil, then finally changed over to redline 75-90ns, correct weight and grade oil, didnt help much with the warm tranny hard to shift problem

ok so after all that, i pulled the transmssion out, (still out right now, just sitting in the garage), dad thought he messed up something when he was doing the clutch, from a glance everything seems fine (flywheel was burned, but wasn't replaced along with the clutch, but that shouldnt cause the hard shifting problem)

so now i'm stumped, cause before we dropped the new rebuilt XJ motor in, we didnt have the problem, dad says kinda happened overnight, so i dont suspect the transmission to be a problem, unless there's something i dont know of........or my diagnosis is wrong.......HELP????
never touched to transfer case, so dont think there's a problem there

sorry for the long read, starting to get desperate, dad's thinking of replacing transmission just for the hell of it