Yeah, 1979. When they added the computerized emissions sometime in the early 80's, they just added more stuff (computerized timing, a computerized carb and all the sensors etc) on top of the old engine. The old 1979 or so engine is still underneath there.
For the computerized system to work right, it all has to be there and working right. That's never going to happen for you.
So, do the Nutter bypass (which bypasses the computer) and then tune it like it is a 1979. It is what lots of people do. Mine was totally stock and had all the parts when I bought it, but hadn't been maintained, so that's what I did. It had very similar symptoms to yours, which I suspect was a failed knock sensor among other things.
When you get to do the tuneup part, use better Ford parts. http://www.jeepforum.com/forum/f8/i-...nitive-669495/
The 1970's ones did have the CTO, Vapor Canister and EGR valve. I'd try to put those back if it was me, because I care about the environment if it is only a hundred dollars or so, but others will have different opinions. But get it running right first.
Many manuals here. http://www.jeep4x4center.com/knowledge-base/
Another viable choice is to buy the kit and convert it to TBI fuel injection or do the junkyard parts equivalent. I have no first hand experience with that. But you'll never get the stock system to work without the stock carb and an unbelievable amount of screwing with it.