Jumpers are not enough. Now inline with juper you have ~500Ohm resistors. Usual way is to use another 500Ohm in parallel. Resulting 250Ohm. It because inside VAG COP has ~400Ohm pulldown resistor for signal.
Could you wire up COPs in wasted spark mode and use stepper chip?
What relates protection: take care to connect secondary winding grounds separately to prevent , but power grounds of coils - near where you have VEMS grounds.
Gints