Once you've encountered the hard start, the ECU is no longer part of the problem. Fuel has wet down the cylinder walls, reducing compression, and the plugs are fouled with fuel. I'd hesitate to use the starter fluid in the manner you are suggesting. It is not intended to be sprayed directly into the combustion chamber thru spark plug holes. Combustion is about the correct air/fuel ratio. Spraying starting fluid directly into the combustion chamber runs several risks, including creating the flooded condition again and contaminating your oil even more.
Crank it with the Fuel injection fuse out util it starts to pop, (this means the air part of the air/fuel ratio is getting back to normal), then put the fuse back in and return to 3/4 throttle and cranking, AFTER trying a normal start process first. Don't forget to rest between attempts, cranking only 10-20 seconds at a time and cycle the key off when you stop to shut the headlights off again. Kill switch off, key off, wait 30 seconds or more, key on, kill switch to run, crank the starter. The car battery is a good idea as it will avoid running down the bike battery, just use normal caution when jumping the two batteries together and during the un-hook stage to not ground anything improperly. Thank you EricV