Are you having problems with the indicator on the column, or actually shifting? If it's not shifting as selected, the only other place you should check is the actual selector on the transmission. Follow the linkage, the selector is on top of the tranny on the driver's side. The selector is a post that sticks up out of the transmission, the linkage rod spins that post to select gears. The post itself is round with a flat spot on one side, the shift rod connector slips over that post with a corresponding pattern that aligns with that flat spot. The pattern on the thing that slips over the post could be worn out.
The YJ is no longer my DD. I have sacrificed all future retirement plans for jeep parts. I'm depending on social security!