alpina 6.0 supercharger project

super spring headers? Man...you are doing this right! How on earth did you land that 6.0L alpina engine?

csi Rider: EWS might prevent you from starting the engine but it should not affect diagnostics... Double check whether the DME is properly grounded, gets power (permanent & switched) and the RxD/TxD wires connect to the diagnostic plug.

By the way, you may not have chosen the easiest engine to mate with a manual transmission. That engine came from an E38 mated to an automatic transmission. Unlike older engines like the M70 and M60, the M73/DME5.2.x has a much tighter integration with the EGS transmission control unit over a digital CAN bus. The engine may refuse to operate normally (ie limp home mode or perhaps no start at all) if it can't communicate with the EGS (assumption, I don't know for sure). The problem with the M73/DME5.2.x is that it was offered only with automatic transmission. So there are no manual transmission cars to swap the DME or the DME programming with. It can be done, though. I recall a 6-speed E38 750iL project by Koala Motorsport and as far as I know they used the original DME. You may want to get in touch with them.

I think revtor might be on to something.
You may have to trick the car into believing it is in N or P all the time. Remember that a car with an automatic will only start in N and P so that might be what you need to do.
Going from old memory I believe people who did manual conversions on E36/E39 put a permanent 12v input on the pin that tells the car its in P or N.

Revtor may actually be able to help you with pin numbers, not sure if that would be on the DME or the EML though.

On a side note, my Supercharger story finally came to an end today.
With help from a skilled local tuner my 850i 5.0 M70 now produces 426 Wheel HP and 600nm.
Depending on how you want to calculate drive train loss the engine is producing between 470-490hp.