[Staylo]

Sounds like you are on the right track. I will bet that your tranny is leaking from the output seal.
As for the idle, continue to look for vacuum leaks. Cracked exhaust manifolds are not uncommon on the 4.0 I6. Check around the flanges well.
IIRC, the 231 command-trac is the base model PT 4x4, the light may not come on when engaged as it does with the 242 select-trac. Put it in PT and do some slow circles in a parking lot, you will know if it is engaging or not. Good luck.