You didn't have a V6, you had an I(Inline)6. Wranglers didn't get a V6 until the 2007 JK's, which got a weak-ass minivan engine that has since (2012) been replaced with Chrysler's new high tech Pentastar design, which is getting good reviews. http://en.wikipedia.org/wiki/Chrysler_Pentastar_engine
The 4.0 litre I6 that you had was based on the 258 cylinder that, I think, was developed under George Romney's stewardship of AMC, and is arguably his only positive contribution to the automotive industry. 
http://en.wikipedia.org/wiki/American_Motors
In all those years, they never did really come up with a good auto transmission to go with the I6. I expect I'll have to have mine rebuilt in my 06 LJ soon enough, as I did twice with my GC. 
Very few vehicles are defect free from the factory. The problem with Jeeps is that their owners love them, discuss and analyze their their woes to exhausting detail, and grudgingly fix them, if possible. People that don't love their vehicles just get rid of their problems and move on. It gives Jeeps a bad reputation. 
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