Well I finally won. All the problems ended up being from a Bad coil. That would have cause the Cats to go bad since it was running raw fuel.
I kept getting a code of a Miss on Cyl #1. So I moved the coil to cyl 5 and the miss moved to that Cyl. Yesterday I picked up a Coil and put it on. No more Check Engine Light anhd the transmission is working great..
Hopefully by the end of this weekend the Jeep will be 100% too, My head should be back from the Machine shop on Friday. Having that Broken bolt taken out and he is going to go thru it. Real good Machinist and its only going to cost me around $100 as long as the Valve guides are good.