Finally put the interior back together today. Looks completely stock! The PCS unit is behind the dash above the center vents where that USB cable is going. I also took the opportunity to install some USB ports and power outlets while I had that panel out. Still need to run the power wires to the inverter in the trunk, but that's a job for another day, or month...
Unfortunately it seems the transmission I got has some issues. I think it might be the broken pressure regulator spring common in the earlier units. I'm going to pick up the spare's valve body at my moms next weekend and do the sonnax kits on it before swapping it in. Hopefully that fixes it because I do not want to have to get the trans out again!
Big thanks to whipplem104 for all the help throughout the entire process (and the controller)! If anyone else is considering a swap, definitely give him a call.