Situation changed!
I have a new (Used) ECM which now lights the "check engine" for about 5 seconds when the key is turned on (like it should). The original ECM, and another borrowed ECM did not do this. I also now have 5V at all the sensors, (red/w wire). With the original ECM, voltage was low, 2.7V or so. The "new" ECM also allows me to run codes unlike the original, (probably fried the original unit with the short in the picture). So when I pull the codes I get 44, which means BAS issue. The red wire supplies 5V to the BAS (and all other sensors now), the ground wire checks out good to ground with ohm meter and passes all wiggle tests. The light green wire also shows good resistance with the ohm meter with no shorting to ground including wiggling the harness during the test. This wire goes directly to the black? connector (from memory) and seems fine. I'm guessing this is the wire that provides BAS feedback to the ECM, so I was particularly thorough checking it since this, (to me) it was likely giving a false signal to the ECM that the bike was on it's side. If I don't find the answer soon it WILL be on it's side with me jumping up and down on it!!
So, I'm stumped. I've made progress in that the ECM seems to actually work, but I'm concerned that I may not have found the thing that killed the original ECM. I've stripped back the wires to the black ECM connector again to double check I have not missed any other chafed wires; not that I'm seeing a problem in my testing.
I know this does not answer what you wanted me to test, but the new ECM is getting different readings from the post you were responding to. I can try to check when I get home, but I'm pretty sure the grey wire is a full 12 V now with the new ECM. The fuel pump still does not run when key is switched on. (No fuel in tank yet).