Here's another update of me spending more time on things that don't really help get the car back on the road.
I've come to the conclusion that I'll have to use the original S13 climate control boxes due to the enormous size difference from the Q50/60 ones. I'll lose dual zone functionality but that's acceptable, so I just need to get the boxes back in so I can fill the radiator with coolant and work on the blend door mechanisms later
While the boxes were out I took a little time to fix my blower fan issue, Q50 blower motor and squirrel cage fan are too large to fit in the S13 boxes, and the S13 fan won't fit over the Q50 motor. After some measurements I CAD/printed a PETG adapter and new fan that would let me adapt the two together.
s13 fan on left, q50 on right
s13 housing
q50 housing
adapter
We also bought a new comically large CR-M4 printer, makes this fan look tiny on the bed.
So far so good, air output seems about the same, we'll see how long it holds up in the car.