After tracing out all the wires in the HVAC harness I think I’ve figured out the source of the problems I’ve been having. Somehow I managed to switch around 2 wires (one blue, one blue/black) on the control panel, and the smoke I saw was a resistor giving up the ghost, not the fan switch at all.
I fixed the wires and replaced one fuse which had blown, but I’m going to need at least a new A/C control panel (I could probably replace the resistor, but it got hot enough to discolor part of the board so I’m just going to find another one) and possibly a new mode actuator before everything will be functional again.
I also managed to get the rear defog wired up, I set it up to bypass the WRX body integrated unit and use the original Legacy on/off switch. It is still connected to the ECU though, so I can use it for logging.
In other news I managed to get the sway bars and brakes fitted, decided to use stock WRX calipers and rotors (thanks Dave!) for the winter and take my time rebuilding the wilwoods properly.
The downpipe gave me a little trouble, as one of the turbo studs refused to cooperate and stripped out the nut. Luckily the thread in the turbo weren’t damaged so everything went together smoothly with a replacement stud from Subaru.
I filled the engine oil (Royal Purple 5w30) and transmission (Subaru Extra-S). Still have to fill the rear diff, power steering fluid and coolant. I’ll probably wait until the interior is a bit more together to tackle bleeding the clutch and brakes, or at least until I can get the driver’s seat bolted in.