The TRE mod in the 'how to' is well written and illustrated, but I think making it more difficult than it needs to be ...
You can attack exactly the same wires at the CDI/ECU unit itself, and all you need to do there is lift the rear seat and unplug the wires from the CDI/ECU; not take half the bike apart to get to the same wires, but under the tank!
Anyhoo
Have you tried a 'reverse bleed' on the brakes?