A lot of good info, but I'm not clear on what the symptoms are at this point other than little to no brake torque.
1. What's the pedal feel? High and firm, low and soft, somewhere in between?
2. When bleeding the brakes at each corner, do you get a nice squirt of fluid when you crack the bleed screws or is it a pathetic little dribble?
3. You mentioned doing a recirculation type bench bleed on the master cylinder, which is fine, but doesn't provide any positive feedback as to the condition of the MC. If you plug both outlet ports and test the MC, you can at least determine whether the MC is good or not. Once both ports are plugged, the MC should hydraulically lock as soon as the seals on the pistons cover the ports into the reservoirs...if it doesn't, then it's still got air in it or one or more seals are internally bypassing fluid. Stroking the piston and allowing it to fully return to the snap ring is a plugged-port bleed, which you should do until the unit hydraulically locks when you try to stroke it. Once that has been achieved, apply moderate force to the piston and hold it for a 20-count, noting whether the pedal (or piston if by hand) sinks over time. If it does, rebuild or replace the MC, as it's internally bypassing fluid and DOA.
4. Once you have a bleed MC on the firewall, connect the rear brake circuit and bleed it. If you have a combination valve with a pin to override the shuttle valve/switch, then make sure you do that since you won't be getting pressure to both sides of the valve. Some companies offer a plastic tool that you screw into the electric switch port that pins the shuttle into place.
5. Once you have a good pedal with the rear brakes only, connect the front brake circuit to the MC and bleed it just like you did the rears until you get a good pedal. Doing one circuit at a time reduces the number of variables in the system at any given time and simplifies troubleshooting if there's an issue.
Tobin