So it cranks just fine, but only has 3v at the coil when cranking and gets a full 12v when jumping the relay. Is that correct?
If you remove and look at the back of the ignition switch, you'll see IGN1 and IGN2.
IGN1 is the run position and sends voltage through the ballast resistor to reduce voltage to the coil. IGN2 bypasses the resistor during cranking to give a full 12v to the coil for start up (which you don't seem to have). I'd check the switch, connections at the switch and at the bulkhead connector as well as the ballast resistor.