I have an '05 LJR with the dreaded infamous NSG370 6 speed manual. I have no issue with CELs. I addressed the OPDA issue as preventive maintenance. I did have the reverse issue with my NSG370 that causes many to replace it with a 5 speed. I replaced mine with a freshly rebuilt NSG370 that has no issues whatsoever at least not yet. I'm confident I won't see the reverse issue again FWIW.
I did recently get a CEL for an O2 sensor, with about 110K miles on it. I replaced all 4 with the recommended NTK sensors. CEL is gone and it runs perfect. Seems to idle a little smoother than before but probably my imagination. O2 sensor fault is a very typical failure that occurs eventually in any vehicle that has O2 sensors. I think every vehicle I've owned with O2 sensors and >100K miles has had a sensor go bad. Hondas, Chevy, Jeep, doesn't matter.
My steering box also started leaking not too long ago. Not sure what years have this box but these steering boxes have a poor reputation. That problem could have been resolved (for a while) with a parts store rebuilt unit. However, I opted for what I hope to be a more durable fix with hydro assist options, the PSC big bore steering box. Pricy but should solve the issue permanently.
IMO, the horror stories about the '05 and '06 model years are WAY overblown. Most of those stories come from people who have never owned one. I wanted a LJR with a manual transmission so choices were severely limited as to the year. I knew about the few well-known issues and they seemed easily solvable. So far they have been easily resolved.
I have no regrets and have never wished I picked something different. The repairs done to keep it running its best seem pretty consistent with what I would expect on any 17 year old vehicle, especially when you consider the type of use it gets off road.
YMMV.