You're giving good info, but I am trying to follow how you are getting your readings.
Anyway, let's just use the Spartan wires and none of the factory stuff at the 60 pin.
Supply 12v thought a fuse to the Red Spartan wire
Ground both the black and white to the battery
Using the battery as ground measure the output of the green wire, with Green being positive and batt negative on your MM. Hook up the MM and put it in view so you can watch the voltage from the moment you key on.
Doing it like that takes the Megasquirt and your stock wiring completely out of the picture.
Anyway, let's just use the Spartan wires and none of the factory stuff at the 60 pin.
Supply 12v thought a fuse to the Red Spartan wire
Ground both the black and white to the battery
Using the battery as ground measure the output of the green wire, with Green being positive and batt negative on your MM. Hook up the MM and put it in view so you can watch the voltage from the moment you key on.
Doing it like that takes the Megasquirt and your stock wiring completely out of the picture.