Funny you should bring up the Nutter Bypass. Yes I've done it to my Jeep along w/ a Motorcraft 2100/ 2150 carb (about $290 and the ign coil upgrade) All well worth doing!! The 2 problems that the YJ is known for is a weak ignition and a terrible carb!!! So the ign and carb upgrades make a huge difference to the way it runs!!
I thought that the Nutter Bypass may have been part of my electrical issues because I may have disturbed one of the grounds when I did the upgrade; or the way I did it. Did all of the upgrades, all at once when I installed the reman engine on a Jeep that bought 1 month earlier w/ a blown engine. No history; didn't know if the Jeep was "straight" electrically speaking before I ripped into it. This last electrical problem I had; had me scratchin' my ass for awhile!!
The ground wires that were really important; that corrected my problems; were the ones associated with the starter relay.
I'm just getting into Jeeps too. I've just had maybe 3 more months experience than you. I've gone thru some of the things you're experiencing.
Good luck and if you need help....... holler!