my first guess would be input bearing or pilot bearing.
if your positive you thrashed the trans or some component thereof, i wouldn't start making any decisions until i had the trans on the shop floor infront of me.
after getting the trans out and the pressure plate off then you can start looking for worn parts.
look at the pilot bushing, if it looks burnt or has scoring in it it may have been your culprit. in my opinion i never drop the trans and not change the clutch disk, t.o. bearing, and pilot. they are cheap enough and you know they will be fresh and hopefully not have to make you drop your trans again any time soon.
then the next thing i would do is grab the input shaft of the transmission. try to wiggle it around, if you get much movement at all you probably have a bad input bearing. this could cause some noise and possibly vibrations and rough shifting if it's bad enough.
one thing i just thought of...
you may be getting vibs from the driveline. when you dumped the clutch you may have tweeked a u-joint. i would also check them for wear and if any of them have some wiggle to them.
this is where i would start... as far as time frame goes...
i can have my trans out in about an hour and a half if i'm by meself. however i have had the trans in and out of my jeep about 5-6 times. i have a pretty good system and all the bolts for everything are brandy new. it takes me a little longer to get it back in without help.
i would plan on a week of having your rig down. it should take less time than that but if you have to order parts then you have a day or so that you can't do any work.
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