What works for many people is to not use resistors. Rather, what most people do when adding LED signal lights is to cut the trace to Pin 7 on the U243B IC. This disables the hyperflash feature and brings the flash rate back to normal. I would suggest you (1) ditch all the ballast resistors, (2)
follow the instructions for stopping the hyperflash, and (3) just let the BEP 3.0 deal with it. FYI,
This thread has pictures of another type of flasher that is found in K-bikes and how to modify it.
What Martin is hinting at is to measure the terminal voltage at the battery when (1) the bike is off (2) when the bike is idling (3) with the engine at 3000 RPM. This will tell you if there is charging going on. We'd expect to see (1) 11.8V - 12.4V (2) 11.9V - 12.5V and (3) 13.5V - 14V. This is normal.
Another thing to check if you haven't yet done so is to make sure the starter has been serviced. Weird electrical problems result if the start motor is dirty or if its brushes are too short. Have you done
that service yet?