The fact that the error code has switched sides makes me strongly suspect the ECU. Ah, but troubleshooting this...
The reason I was able to read the voltage coming from the knock sensors to the ECU was because I had already cut the wires about 6 inches from the gang plug at the ECU. Therefore, I had a handy butt splice I could put the meter lead into. That was a result of being led astray by the misinformation in the Honda Service Manual.
I am not sure about the sub harness but I know that if the big plug is not plugged into the ECU the bike will not start.
My thoughts here... IF I were doing the troubleshooting, I would have 3 options. You may come up with others, they may be better.
1. Borrow someone else's ECU. Quickest and easiest.
2. If you have a service manual and can verify which color wires go to which sensor, (this would mean removing both lower fairings) you can:
A) Disconnect both sensors. Insert a wire into each female plug with a female spade connector on the free end. Criscross the wires under the bike and connect the female spades to the knock sensors. This effectively "swaps" the left and right sensors. Rev the bike up to 4K for 10 seconds and see what code you get.
OR
B) Cut each of the sensor wires about 6 to 8 inches away from the ECU gang plug. Using wire nuts (because they are temporary) criscross the two wires and reconnect them. Rev the bike up to 4k for 10 seconds and see what code you get.
OR
C) Make a VERY SMALL nick in the insulation of each wire, just enough to get the point of your meter probe to touch the metal wire strands. Read the voltage from each one. When you are done, a couple wraps of electrical tape over the removed insulation and you are good as new.
None of this will be fun or easy. If I have not explained this properly, PM me. Or, I will be watching this thread. If necessary we can swap phone #'s and perhaps I can explain better over the phone.
Good luck, let me know how I can help you.