So, JTH0033, you put the Motor Craft carb on and didn't do the Nutter bypass? Because if I understand you then this would probably be a major part of your problem. I have done the nutter by pass myself, and as I understand it (which is fairly well) the point of the nutter by-pass is that your computer is no longer messing with your timing so that you can then set your timing and it will run like a "normal" carbureted vehicle. And, as of = now since you haven't done the Nutter Bypass your computer is; 1) freaking out because it probably isn't getting all the info it should get from the sensors, 2) is trying to tune the carburetor for fuel mixture, and last but not least 3) jerking around your timing based off of the assumption that it is connected to all its sensors and the carburetor and still can sense and control what is actually happening with the whole system.
Unless, I am totally wrong about all this then I don't really know how anyone that changes out their carb, doesn't have a means of messing the new one into the emissions system could have their engine run well or ever pass an emissions test where they actually check the exhaust for chemical numbers.
1987 Wrangler YJ RED 4.2 5-speed, NP231, BFG 31x10.5R15 AT/KO on 15x8 gambler wheels.
Caution!!! Under construction!!!!!! Caution!!!
Finishing a 4.0 Cyl.head swap, Just got an AX-15 NP231J combo to replace the busted t-case and craptacular BA10/5. Adding Nutter bypass. Probably more to come before it is back as a DD!