A couple of pics of how the engine bay sits now. The temps out here have been in the mid to upper 90's so it's a good time to work with the cooling system. The radiator was moved slightly to take advantage of more airflow, and that seemed to keep the temps in check.
The boost controller has been reconnected. It makes a huge difference in spool time, and now the boost repsonse has to be felt to be believed. It's so sensative that the pressure can be modulated easily with the pedal, whereas every 2jz I've ever had has been an "all or nothing" situation. I'm going to try and get the car back on the dyno this weekend, and along with going for higher boost, I'm going to ask for a redyno of the baseline 8psi. With the controller hooked back in, and the transmission working properly, I'm betting on a good bit more power. FWIW, as I was messing with the boost controller trying to get it to 8psi, it overboosted to ~20psi. The car is a real screamer.
Here is how the engine bay sits as of now.