Robbie, I'm planing on doing the engine swap in my 07 JK next year but I would like to start sourcing parts as soon as possible. I have a some questions if you don't mind.
1. I currently have a manual transmission but I think I would like to use the 6L80E. Will the tap shiftier from a 2012 JK work? Will it fit in my current console with the 07 automatic bezel?
2. Will I need a new instrument cluster?
3. Will I need a new JK PCM?
4. Will I need new drive shafts?
1. Yes we can support the 2012+ bumpshifter in an 07' but the 12' shifter does not fit into the 07' console. You will need a 2011+ center console. Unfortunately Chrysler has raised the price on the console components so much it will run $800-$1,000 to purchase all new parts. This includes the front and rear console sections, the lid, cup holders, etc.... As far as the console goes look for a take out from a guy who installed a Tuffy or other console. I had a customer get a whole console assembly from a 12' for $75 off eBay.
For the manual to automatic you will need two shift cables, one is for the transmission and the other the key interlock. An automatic brake pedal, the pedal is optional but we like to replace it. No hardware is required as the same pin and clip hold it in. The sled which is the metal plate under the shifter assembly, fortunately these parts are inexpensive from Chrysler.
2&3. No I would run the stock cluster and PCM. Your PCM does not have a C4 connector for transmission control but it is not a problem, our interface controls the reverse lights, neutral safety, etc.
4. Depends on what engine you run and what suspension you have. If you lift a JK with stock control arms the rear driveshaft gets shorter and we already move the TC back about 1". We do have a reduced length TC adapter and with stock suspension you may get way with stock shafts,. The original 5.3 JKU we did in 2009 is still running the stock JK shafts with 130,000 miles. If running a 6.0 or larger engine with larger tires I would upgrade the shafts. In that case we can have shafts built for you at a reasonable cost. Normally we run a 1350 rear and 1350 or 1310 front CV.