Yes, I am 99% positive the wires to the coils are correct. I visually checked and double checked, and ran continuity checks with a voltmeter through every wire to make sure they are going where they are supposed to. Bike red to '+' on 1 and 2, '-' on 1 to '+' on 4, '-' on 2 to '+' on 3, '-' on 3 to bike green, '-' on 4 to bike black. I also spliced the reds going to 1 and 2 together and only connected to one bike red. I believe both reds are always hot (key on) and the igniter completes the ground through the black and green wires when the plugs need to fire, right?
I also ran resistance tests at the harness ends and came up with 2.6 - 2.7 ohms on both circuits, the same as each individual coil (1.2-1.4 ohms).
I did reattach the black/yellow to ground. Should that not be done or is it a "doesn't matter"?
As I look around the internet some more at other bikes' setups, I see that the rubber seal is not needed.
Thanks for the help, Tony.