i have a 94 5 speed command trac with a 97 4.0 h.o. but i bought it like that already converted over. i was told by the owner that he replaced the engine himself and that there was a few electronics that didn't connect, but that he had had no prob. since i have owned it it has had no problems and on the positive side, i believe that it also solves the blowby problem common with the old setup. as far as which connections weren't applicable, i am not sure as i have only owned this cherokee for about a month so far, but i have gone though the engine and i believe i have only seen 2-3 connections that aren't being used right now. most likely this has been from the abs system which my xj doesn't have. I AM NOT AN EXPERT. this is just my observation on my jeep, i do not know if the 98 is any different than the 97, but i do not believe so. it runs well and has had no issues...
riehl8
p.s. i'll try to take some pictures under the hood, perhaps that will help you.. if i can find those unused connections, i will get some good close-ups for ya.