If you go to the stickies at the top of the page, then to the YJ FAQ, then to the engine/ carb section, there are three good write ups on the nutter bypass. I found the one called picture guide to the nutter bypass particularly helpful.
When you replace the carter carb with either the weber or motorcraft, you take the computer out of the loop in controlling the carburetor.
When you do the nutter bypass, you take the computer out of the loop in controlling the didtributor/ignition.
1989 YJ - 4.0L
2001 WJ 4.0L