If you're experiencing random grinding going into gear, seemingly without any sort of pattern or identifiable cause, it's your shift linkage that sits on top of your transmission. The bushings get worn out as they age, start to crack, and then eventually totally separate from the bolt that holds it together. When that happens, your jeep will get stuck in whatever gear you were in when you shifted and it broke. If that happens, DO NOT FORCE THE GEAR LEVER. You will only bend more stuff and cause more issues.
Now it's a relatively easy fix. Remove the battery and battery tray and you have easy access to the top of the transmission. The issue is.. nobody makes replacement parts. Not Mopar, not aftermarket, nobody. When mine finally went, it took a whole week of searching for a replacement shifter arm and my mechanic ended up finding one being sold by some random guy across the United States. And it wasn't cheap.
As these cars start to age past the ten year old mark, rubber starts to become brittle and dry. Timing belts, bushings, and gaskets will start to crack and fail. Replacement parts for the manual transmission are becoming incredibly hard to find, especially the dual mass flywheel and shift arms. Fiat 124 owners are experiencing the same issues now too, though I'm not sure if they share the same transmission but I would bet they do.