This gets stranger and stranger. I had some time this evening and took a chance with additional troubleshooting since I'm pretty dead in the water otherwise. The board powers up fine when A,C,D PCI-E are plugged in, but B is what causes the issue. I see nothing wrong with that connection.
If I try to get the board to hash in this state - I am not sure this is possible - I get the Operation status 20 error and it continuously re-detects the board. I have not touched anything to do with firmware and since it doesn't seem to be helping the others with that problem and I'm not going to try yet. I am wondering if it is complaining because that one isn't powered up and if it is possible to disable a chip. I'm not even sure if things are set up that way - just hoping for some kind of way to get it partially alive again.
Thanks for any help.
It's hard to tell without testing using a multimeter, but it sounds to me like the one input (B) is shorted. That would be why the PSU is shutting off if it's disconnected. You'll get the regulator programming error if you try to start running with the one cable disconnected, but you should be able to leave B off if you set the voltage to 0 for that die using hftool or JakeTri's modified cgminer. The firmware will then route around that die and not turn on that power supply.