2.5L or 4.0L? To access the fly wheel the you will need to remove the trans an TC. While you have access it would be a good time to replace the clutch, thow out bearing and slave cylinder. Also you will easier access to the rear main seal so make sure you check it and make sure it is not leaking.
1991 YJ 4.0L, K&N air filter, SS headers, 31X10.5, Congo Cage, etc...
When all hope is lost, and you have run out of options, you can always break out the "HOLY HAND GRENADE"!!!! It may not fix it, but you will feel a lot better.