If you are getting 12V on the ref+ (yellow/green) wire, this means the ECM internal power supply regulator circuit for Vss-Ref has "gone to the rail" as it's called.
The easiest way to go about returning the voltage back to 5V is to simply repair the ECM Vss-Ref power supply. There is a few different ways the Vss can go to the rails, they are;
1, the voltage diver that adjust Vout is pulling Vset low. This would make the IC output maximum potential that is equal to Vbb+
2, The capacitor C2 is shorted across Vin & Vout pins of the IC which is providing a DC current path around the regulator circuit. Again causing Vout to equal Vbb+
3, the regulator IC is shorted to Vin & Vout.
4, If the regulator is a TO-220 case device the insulator between the case and the heat sink is leaking current. Causing the IC to put maximum potential also equal to Vbb+.
If you have a LM7805 laying around you can simply drop that into the ECM 5Vref supply. Afterwards you will need to adjust C3 to bypass filter the alternator ripple.
If all sounds to complicated, I have remanufactured ECMs in stock available.
