Well the truck got so bad that my company decided to take it to a shop and have it fixed when I was down at the main location last week.
Here is what they found and am surprised I missed it (but dont have someone inside to run the truck while I look at the outside)...
There was a broken motor mount which was stretching and shorting some wires when the motor flexed or when I went over a bump. They replaced the motor mount and the crank sensor (and harness since that is the harness that was shorting I believe...I didn't get to talk to the shop to get specifics so this came third hand).
It is running great again and just figured I would answer my own question in case someone searches something similar.
hard to believe the small amount of problems I have had with this truck in the time I have had it and the mileage I have racked up. Wish they still made the cherokee with the 4L 6.