Well after many side-quests, I determined that the spindle PWM leg on the output buffer chip U3 / SN74LVC2G17 of my SLB had failed - it came off as I was replacing the part. This is what caused some of my confusion while trying to understand all of this. Finally replaced today and I think we’re back in business.
I’ve subsequently figured out how to program a VFD to enable/disable based on PWM alone. I guess at some point I’ll see if I can get the direction signal to work as well, but for now I think this thread is resolved.
As promised, here’s a work-in-progress writeup for converting a C3D Shapeoko 5 Pro 4x4 table to utilize a SuperLongBoard controller. After waaaay too long, I’m almost at parity with the stock controller, just the front plate / probe / tool lenth sensor left to go 
Hopefully these docs help someone else make this conversion with way less headaches.