I've got a 4.0L with the inline 6 motor. Put it in gear and it makes a terrible grinding sound in the passenger side floor board. It makes the same exact sound when you put it in reverse. In reverse it doesn't matter if your moving or sitting still. Put it in reverse and the sound is there and now louder. Does not make the sound at all at hwy speeds. Tranny shifts fine. Everything works as it should, just this loud obnoxious noise. I haven't inspected the flexplate or took off the inspection plate yet...I was kinda hoping someone would suggest ujoints.

 

i dont know much about these particular jeeps but my 2000 xj has the same engine (4.0 I6) to the best of my knowledge i would say its a safe bet to look at the tranny although it may not be making noise on the highway, it could still be a major problem. you could possibly be catching gears and it shifts when you get up to speed. off topic i had a problem similar to this with my 1992 Ford F150 I6 4.9 automatic, and it came down to me having to replace the transmission. automotive problems can be very specific and hard to troubleshoot sometimes. i hope this helps somewhat

 

Could it be described more as a buzzing or whirring sound? I'd start by checking your fluid level and condition, and for leaks. No noise at all in park or neutral?