What is the best year and model of Wrangler?

The model years I would not recommend are 2001-2002 for cracked 0331 head issues, and 2005-2006 due to the possibility of not easily cured problems with the oil pump drive assembly, and the possibility not easily cured of automatic transmission software issues.

If you decide on an automatic as I always strongly recommend if you intend to do lots of offroading on more challenging trails, I'd go for a 1997 to 2002 which has the awesome 32RH automatic transmission. For a 5-speed, the 1997-99 has the very good AX-15 transmission. Then came the not quite as good 5-speed NV3550, then came the not quite as strong 6-speed NSG370.

In summary if I were buying a another TJ I'd buy a 1997-1999, or a 2002-2004. I Ioved my previous (stolen) '97 and my present '04.
 
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...then came the not quite as strong 6-speed NSG370...

First off, Jerry, you’re a legend - thank you for all the helpful posts around.

As an owner of the NSG370 - can you expand on common problems you’ve seen with these and things to keep in mind? I love manuals so was pretty keen to find one I think will do well, but love knowing what to keep an eye for.
 
In my opinion, it’s the 03-04 Rubicon.

I studied this for a while and this is the most common answer to be honest, if you are looking for a manual transmission. I ended up with an '04 Rubi and it is all that it is built up to be. The 6 speed is less desirable and before the '03 there were some issues that have to be fixed by the owner. Can't remember what they are. Anyway, the '04 is probably the most desirable as it is the last year of the 5 speed.
 
I studied this for a while and this is the most common answer to be honest, if you are looking for a manual transmission. I ended up with an '04 Rubi and it is all that it is built up to be. The 6 speed is less desirable and before the '03 there were some issues that have to be fixed by the owner. Can't remember what they are. Anyway, the '04 is probably the most desirable as it is the last year of the 5 speed.

Yes, if you prefer a manual, the 5-speed is slightly more preferable over the 6-speed from what I hear.

If you prefer an automatic, then either 03-04 will do. I have an 05 Rubicon and don't regret the purchase at all. But, like I said earlier, if I ever have to replace the engine, I'm going to swap in an engine from an 03-04 with the wiring harness as well, that way I have a separate ECM and TCM, as oppose to just one TCM.
 
Currently, the 6th gear is a cruising highway gear.

But when you regear.. doesn't that extra gear give you a broader range of gears, which correlates to greater use off and on road?
No. Re-gear based on the overdrive gear and your highway speed. Your 5th is still a direct drive. Everything else is just an extra smaller step to get there.
 
No. Re-gear based on the overdrive gear and your highway speed. Your 5th is still a direct drive. Everything else is just an extra smaller step to get there.

Which means you have a more usable gear set on and off road. The transitions are easier, and the range is broader than a 5 gear setup.
 
Which means you have a more usable gear set on and off road. The transitions are easier, and the range is broader than a 5 gear setup.
The considerations for regearing are the same as any other transmission. Only the ratio is different when compared to a different setup. There are plenty of discussions on this topic.