After the swap, I let the car idle to get the air out of the coolant system. IT took quite a while for the fans to kick in, as the Koyo radiator is quite large and takes a bit more coolant. For the coolant, I used the Subaru coolant conditioner, and Peak Long life coolant, mixed ~50/50 with distilled water. Once I was confident all the air has been burped, I proceed to attempt to move the car out of neutral. With the car idling, I tried to shift the car into gear, initially first gear.
The shift lever however would not let me in. Tried reverse, same result. Poking around the forum, some threads:
Can't change gears when running
Clutch cylinder rod mating to pitch fork
So I tried the method outlined in the first thread and the car ended up stuck in first gear (I couldn't get the transmission out of first with the car off). Out of options I posted my own question: Motor Swapped, new clutch will not engage
It turns out the throw out bearing wasn't sliding on the input shaft. Although it was greased, after reinstalling everything, I did not use the clutch fork to physically slide the TOB to verify smooth operation; it was stuck. Wiggling the fork and the TOB solved not only the clutch engagement but also the clutch pedal engagement which I had thought was due to bad clutch system bleeding.
Lesson learned: make sure to use the fork to slide the TOB on input shaft