An update, just in case anyone reads this thread.
This time when I put it back together and tried to start it, I moved the ECU and everything started freaking out. Wiggling the black connector, things would go from bad to worse. Fan would come on, even though the bike was dead cold. Every sensor related to the fuel injection system was showing error codes. I was able to re-position the ECU and get the bike to fire up. It would run, but was running rough and super rich.
Something is physically broken inside the ECU. Grrrrr.... How'd I get so lucky to end up with a busted ECU and a self-destructed starter at the same time. Luck, it can be interesting to say the least.
Well at least I believe I found the problem, and I can get parts off eBay at a reasonable price.
The harness was the first thing I checked. I went through it with a fine tooth comb, checked every single connector. Probing from both sides, while wiggling wires and had no open or intermittent wires. Putting pressure on any of the wires would cause the ECU to to see every sensor as bad. Barely touching the black connector, with just enough pressure that did not move any wires the ECU would see the same problem. I even popped open the connector and didn't find any loose, out of place, stretched or corroded pins. I'm fairly confident that it isn't the harness and is the ECU. I believe must be a cracked solder joint on the pin connector inside the ECU. It just took 42000 miles and me messing with it to actually fail enough to cause issues.
Anyhow, the parts I ordered are on the way, and hopefully that solves my issue. Fingers crossed.