YJ, initialization is a handlebar procedure required anytime the TPS, ISC are replaced according to the service manual. Also works for any departure from computer controlled idle of 1600 +/- 100 rpm, surging, whatever is NOT smooth idle. It goes like this: parked on centerstand, sidestand up, ign off, start-run in run, throttle wide open, key on (no start), eight seconds later from key on throttle closed, key off, throttle closed. Try normal start, check idle. Repeat above if idle is not right. Hey, did I get that right, y'all? I would leave that idle stop adjustment alone since it is not an idle setting like on a carb.
Karl