Thanks to my trusty multimeter, I found the problem and have fixed it!Hmm, I'm a bit perplexed on this one. Sadly, I sold my 06' that I did this mod on almost 3 years ago now, so I can't offer any advanced trouble-shooting. If it were me, I'd double check the wiring manuals between the regular 6 and the MS6. Perhaps a wire is loose or you have a bad splice somewhere. No power to the main driver switch leads me to believe it's not receiving power from the circuit feeding the master switch.
I am not sure where the error lies, but the two RED/YELLOW wires in my driver door harness had to be swapped at the body connector. I don't know if I mixed them up while re-wiring the master switch connector, or if you mixed them up while writing the instructions.. but I was getting power through the wrong RED/YELLOW wire. Apparently the circuit within the master switch still allowed this power to run through to the other RED/YELLOW wire over to the passenger front switch because unplugging the master would kill the power to it as well.
Fixing this error also powered up both rear windows bringing successful auto up/down function. (however I have determined that my driver rear switch is not working correctly and am getting a refund.. searching for another!)
Also, using ms6 rear harnesses, only two pins in each door connector had to be moved.. making for a much simpler mod for the rears. I did not use a ms6 driver harness but it appears that would be a similarly "simple" modification, only needing to add some wires to the main connectors from a donor harness, only splicing two pairs of wires. I will figure this out and post a supplement for anyone who would rather go that route, since ms6 parts are becoming easier to find these days.