Interesting. This makes me realise that there might be something fundamentally wrong about the diagram I gave you for the 'diode and resistor' circuit.I started to tune and found my cranking RPM's were about 800?
A little history is appropriate at this point:
The circuit is actually the work of Matt_gsxr who was pretty active here on the Megasquirt websites for a while, although I haven't seen him post lately. I took the diagram of his circuit (the drawing of it is his work also) and I modified it slightly for my project which is an inline 2 cylinder motorcycle engine with wasted-spark and a 180 degree crankshaft (a Kawasaki EX-250). I knew from looking at Matt's drawing of the circuit that I didn't need both of my bike's coils connected to the OPTOIN+ because of the wasted-spark nature of its ignition system. So when I installed it on my motorcycle I only hooked up one coil (just used one diode and one resistor). I knew this would work on my 2-cylinder because its wasted-spark ignition system fires the plug every time the piston approaches top-dead-center, which means that only one coil needs to be hooked up via the 'diode and resistor' circuit to provide the correct RPM.
I've never worked with an inline 4 cylinder motorcyle engine like your CB engine, but now that I've read your latest post I've realized that for a fuel-only Microsquirt application you need to do the same thing that I did. Reduce the circuit to only one coil and it'll work perfectly. Because a wasted-spark inline 4 fires its plugs exactly the same way as a wasted-spark inline 2.
I think that Matt_gsxr was working on a motorcycle engine that was coil-on-plug and therefore wasn't wasted-spark so he had to pick the correct two of the bike's four coils to hook up with his 'diode and resistor' circuit to get an ignition event indication to the OPTOIN+ every 360 degrees of engine rotation.