Good question....it can sure seem overwhelming when you stand back and look at the whole thing.
Start small.....clean things up, take lots of pictures for future reference.
There is an access port on the top of the bell housing and you can take it off and look in there....
Also the shift tower unbolts from the transmission case and you can look around in there...sometimes it is full of water so don't be surprised or discouraged.
Once you get the drive shafts off you can spin the axles and listen, feel for rough bearings.
Drain the engine oil and look for water or small bits of metal.
I would give the mystery oil plenty of time to work. Some use a mixture of Automatic Transmission Fluid and acetone....
The transmission and transfer case are pretty simple, lots of guidance in the tech section of the home page.
http://www.cj3apage.com/index/Tech_Tips.htmYou can do it...be sure to take lots of pictures!
Randy