Isn't the 06 TJ manual transmission "NSG370" the same on JK manual transmissions ??
I want to change my auto trans to manual and used manual trans are even costy $$$

 

I swapped mine from auto to manual... Needed new upper wiring harness, new PCM, tranny, pedal assembly, console, and various other parts.. Then bring it to the dealer and have them reflash the manual PCM to your ignition Whig they were reluctant to do for me as they have never done anything like that. My swap has 23k miles on it now problem free. I was lucky and found my whole swap.. Almost every single part as a lot on this forum. If you don't find a whole swap (someone taking out their manual setup and going to auto), I recommend not doing it. Even with all the parts and a lot of prayers and about 20hrs of labor, it was all still a crapshoot.