Does it have the 2-bbl Carter with built-in stepper motor? I know my brother's '85 CJ7 with the 258 has the same setup as my '90 (the above mentioned Carter and the electronic emission controls) and we did the nutter bypass on it to clean up everything that you mentioned. Just do a search on here for "nutter bypass" in the CJ and YJ forums and you'll find a whole bunch of info. If you have to keep emission equipment for your area, the carb may simply need a rebuild (about $12 for the do-it-yourselfer) and although it won't get rid of all the vacuum lines, it may run much better. One important thing, based on the age of your jeep, the stock carter carb may be worn out--they leak air around the throttle shaft with time. I got 130k miles out of mine with one rebuild at 80k miles, for reference. (personally, i'd replace it with a weber, as evident in my sig, if necessary--much less temperamental).
Currently an '86 CJ-7---following a string of '01 Sahara, '90 Sahara, and '85 CJ-7. Finally got back to how it all began....