If you plan to keep the OEM Carter, then you need to keep all of the emissions equipment in shape and working well. This is one of the big reasons many people (including me...) dump the Carter. What many people thing is a problem with the carb is actually a problem (or series of problems) with the spaghetti mess of emissions equipment on the early YJs (and late CJs for that matter). Even one sensor, switch, or vacuum hose out of whack can wreck the whole deal and make the computer take a dump, causing problems.
Despite what some people say, keeping it all running well can be done, and it's really not too hard - just somewhat tedious. You need to know this information...
...up and down, inside and out. When I first got my 1990 with the Carter still installed, the information on that page was a lifesaver.