Since then I have spent every bit of free time checking the transmission electronics, sensors, etc and make a conclusion that the transmission was defective and went to remove it today. I was just about to remove it, when I had one last burst of idea about the Torque Converter. I had my old transmission sitting behind me and I decided to measure the distance from the TC to the hole where the starter used to be. It turns out the TC was too far out of the transmission, buy 5/8 of an inch! It turns out that is also the same distance as the teeth on the TC that connects to the ATF pump gears! So all my frustration for the past week has been caused by me not installing the coupling properly!
This afternoon I reinstalled the motor, this time with the TC properly set (I hope) and did a spin up and I could now hear fluid flowing through the transmission. Tomorrow I will reinstall my control systems and give it a drive around. I still haven't spent any time with the Zilla, but if tomorrow goes alright, I can start on the Zilla this weekend.