Well, I took the plunge:
I followed my plan of making clearance for the socket head cap screws on the upper mount locations. I had to grind back on the ribs a bit to make clearance for both the bolt and the hex socket that I used to tighten down the bolts. Still seems like there is plenty of meat on the case, and I didn't get too close to any of bolts that hold the adapter to the transmission. I also had to drill out the threads in the upper holes on the Novak adapter.
I used the stock GMC clutch, pilot bearing and throwout bearing and it all appears to be functioning properly. Driveshaft is being built so haven't driven it yet. The original Comanche shifter looks like it will hit the seat so I'm going to have to do something different with that.