sounds like the shift linkage is out of whack. if you crawl underneath the jeep, you'll see a rod coming off the t case that attaches to the shifter linkage. there is one bolt there, if you loosen it, you should be able to get it back where it belongs.
the tires never barking in any position sounds like you might have CAD issues. theres a sticky relating to it in the YJ forum.
'90 YJ, ford 8.8, SOA, lincoln front, aussie rear, 4.88s, swampers.