Quick updates to this ongoing saga:
DY suggested looking at the grounds. Good idea, checked them by measuring high current voltage drop, they are fine. I also took out the BMW wiring CD. The grounding is certainly not obvious. In stock condition, there are four ground wires that connect to the battery and only one of them is a direct connection to the transmission. At some point I will do a thread on this. However, the Motronic, Alternator and Generator all get their grounds from the transmission/engine connection and as a result, any drop in the large cable from battery to transmission would affect measurements and operation.
Today I connected the fuel injectors to a car battery with the car running, adding a volt to the injectors during my cold start test (12.4V to 13.4V or thereabouts). With everything else connected normally, the battery voltage low as it has been. The motorcycle started quickly and ran smoothly. So the cause of my problems is low battery voltage during starting and the effect is lower voltage at the injectors that the Motronic can't/doesn't compensate enough for during starting, which is Open Loop operation.
Also, I discharged the battery for 20 minutes with the headlight, rode the motorcycle for an hour. Came back, turned on the headlights, lo and behold, the battery voltage with the headlights on but the bike not running was 12.5V for 5 minutes or so. This is 0.4V more than I have recorded in any log that I have in the past year for the same condition.
So it looks like GSAddict nailed it, the problem is that I've undercharged the battery for the past year and a half. I will discharge/charge it per detailed recommendations (that I'll post later) from Odyssey.