No convincing needed. I did enough pre-purchase research to know I wanted a LJR with a manual transmission. That is what I got like 5 years ago and nothing since has caused me to second guess that decision. I have what I want/need for my type of use. No regrets. I really can't think of anything I would prefer to own within the wrangler family. The few tradeoffs to get this configuration were and are a small price to pay in my judgement for the utility and capability provided.
My goal with this thread was not to convince me of anything. I was motivated by the constant and, IMO, unwarranted trashing of the 05-06 TJs and the associated misinformation. I know a lot of folks, like me, do a lot of research on forums like this before making a purchase, as I did. There are certain folks on any given forum who tend to have more weight given to their opinions on things. On this particular forum, one of the most respected members is also a primary source of negative shade thrown at the 05-06 TJs. I think that is likely scaring people away from some great purchase opportunities.
I know my Jeep well enough at this point that I don't expect any surprise failures. If it ever leaves me stranded, I might change my opinion. But in my experience, a huge majority of potential failures are easily anticipated and preemptively avoided which is how I try to operate.
I am still curious on 2 questions though. Maybe I just missed the answers (as opposed to guesses/assumptions) on these questions.
Is the fuel tank check valve issue only on the 05-06 models?
Do manual transmission PCMs on the 05-06 models fail noticeably more frequently than PCMs of other years? How likely is a manual trans PCM failure on the 05-06 TJs?
Otherwise, pending these 2 questions, I think the list in my original post may be the actual list of unique 05-06 issues. Not so bad IMO. To me, definitely worth the price of admission.