The issues you are seeing with the Faders and the Vpots not functioning are likely caused by the 12volt motor supply ground not being referenced to the digital (5volt) ground. Both the faders and the Vpots use separate 5v linear regulators on each board to provide a stable reference. There is also a regulator on the brain board that provides a reference for the A/D convertor. These regulators are fed from the 12v supply,
BUT referenced to the digital ground rather than the motor ground, so there needs to be a connection somewhere between the two grounds. Quite where this connection is on the stock D8B console and CPU is not clear from the schematics, but it must be there!!
Ralph's
instructions for the console power supply show a link between J201 & J101. These are the motor and digital grounds, so I'd guess that the grounds on the stock setup are connected somewhere within the CPU.
Edit: Having read through the thread again, arjepson noted the above as well. He comments that:
I have the M-gnd connected to the other grounds through a 100R resistor, to a have a bit of seperation.
As the only current that would flow through the resister would be the ground currents of the regulators, it will not be much (5-6mA per regulator at a guess). If you want to be able to use the console with an original CPU, I'd join the digital (5v) and motor (12v) grounds in your new CPU. Joining them inside the console would work , but if you were to go back to an original CPU with the grounds joined in the CPU as well, you will run the risk of introducing noise into the digital ground from the motor ground.
Hope that helps
John