To clarify
The trigger rotor fits on its shaft only one way, this is determined by its small locating pin, agree?
The cog that engages into the camshaft can fit on the beancan shaft either way, at 0 or 180 degrees, right?
This one makes no difference.
I can post pics later if you think I'm not explaining it right
Different part number ECU's have different internal electronic specifications that will vary depending on the system's hall sensors (type, quantity, sensitivity, impedance, etc) and depending on the ignition coils (type, quantity, resistance, output, etc.) and depending on the rev limit established by the manufacturer for any given application. They might also vary depending on if it's a 1, 2, 3, 4, 5, 6, 8, 10, or 12 cylinder engine. I do not believe there is any internal circuitry that advances or retards the timing in any of these ECU's.
If you're getting a STEADY AND CONSISTENT FAT BLUE SPARK AT BOTH PLUGS, while cranking the engine with the starter, most likely your ICU is OK.
BUT
If that spark is not occurring at the right moment, even after rotating the beancan throughout its range, you most likely have an internal beancan advance mechanism problem. Something might be missing, stuck, jammed or bent.
If that inability to time the spark was caused by excessive timing chain wear, I think it would be (horribly) audible.
If the bike had always run terribly (since you've owned it), it is possible that the previous owner replaced the timing chain without properly aligning the camshaft and crankshaft, but I doubt that.
The reason I suggested direct(hot) wiring the system for testing is I that I have personally experienced issues with kill switches, ignition switches and faulty harnesses that caused weird things to happen to the ignition electronics and wanted to eliminate those possibilities.
Hope I'm making sense to you,
Keep me posted, we'll get to the bottom of this, by hook or by crook
I will walk you through this step by step if you want. Just say when...