2006 Wrangler 4.0, swapping 42rle out and Full manual control 700r4 in, need info.

Hello all,

I have committed to full send with my course of action and now need to figure out how to make everything work. I had a full manual vb, reverse shift pattern 700r4 built to the teeth to put in my beloved 2006 LJ. I?m currently mating it to the 4,0 and a freshly rebuilt 231 transfer case. I have the Hesco unit to relocate the crank trigger to the front pulley. I can figure out the fabrication and mechanical stuff pretty decently I think, but I?m stuck with the electronics, particularly the PCM. I was going to go with a stand alone but HPtuner seemed to have the bases covered for my needs just as well for the time being so I gave it a shot.

My main question/concern is whether or not I can simply write my 2006 AT PCM to run a mechanical 700r4 in manual mode and have the stock TCM stuff completely disconnected or will I need to buy a manual PCM to do this? If I cannot delete the AT function from the 2006 PCM/TCM it will put the engine in limp mode. My next question would be how can I most easily accomplish this? Lastly I need to know how to obtain a file to start with or do I need to write it from scratch?

Please keep in mind, I?m 51 years old and I love machines. I have been wrenching on, building, and obsessed with machines since 1974. That said, I know next to nothing about many parts or how they operate, particularly computer control. I can grasp the concepts and I?m sure I can learn, but it?s not my primary language, just so I?m clear. Thank you.