Would having the Dyna III ignition wired up have anything to do with how this got "messed up"?
I get the idea that color coded wiring should make this super simple. However, there seem to be a couple of extra green wires. If memory serves me, I think one daisy-chains out of another connector on green wire. I am fairly certain that all the wiring on the left side (as you look at the board) is fine. I believe it's the green wire on red, in conjunction with possibly a few other wires on the right side of the block that are messed up.
If I can't get it right, I'll consider finding a stock board. I am just guessing the OP put a new board in when he put the Dyna III in.
Riding my airhead is like eating chinese food . . . an hour later, I need to ride again.
1978 BMW R100S "bitza" (R80/7 frame)