Most of the wiring can go.
Since you have swapped carbs, the computer is no longer doing anything for the most part.
Start with the Nutter bypass. You can skip the carb setting part.
After the initial ignition wiring change (making sure you have started and timed the engine) I disconnected the computer connector and started pulling the wire to their ends. There are a few you will want to leave connected (manifold heater and relay and choke) but every time I cut a wire if I had to to remove it from the tangle, I started the engine. Whole lot easier to know what wire cut screwed things up than trying to figure which one of many did it.
Check this site for what does what. http://home.sprynet.com/~dale02/list.htm
It also explains the Nutter. http://home.sprynet.com/~dale02/ignmods.htm
You will end up with more wire, tubing and relays on the floor than in the CJ.