Hum, interesting problem. Several comments:
1) The green stripe modules are the *old* ones. Yet you have the "new" 2x6 pin connectors. IIRC there was rather a mix of old/new versions around the same time they switched to the heavy case versions in about 2006. Kind of crappy for Rotax to do that, but I guess they had an excess of old modules laying around.
2) Trigger coils can pass a resistance test, but still fail to work properly. Reason? The permanent magnets can get weak over time, especially if they ever got too hot. This happen to me with the crank position sensor on my 1998 Ducati.
3) Your description of the increasingly difficult starting is exactly what I experienced a couple of months ago. What I found was that after "professional" overhaul, the float arm adjustment was way off, allowing too much fuel in the bowl. This flooded the carb, so it wouldn't start with the choke engaged. The same effect would happen if floats were sinking or fuel pressure was too high or if the bowl valve were sticking or defective. Once running, it seemed fine, but the plug colors told another story.
4) 4) Soft start. The old start circuit set the timing to 4 degrees BTDC which gives an “angry” start and risks kickback which may destroy the sprag clutch or starter. The new modules use 3 degrees ATDC which eliminates these problems. Both set to 26 degrees BTDC while running. Soft start modules work on the old engines if one adds a wire to the starter which triggers the function. But, to get full benefit, the flywheel must also be changed. The bumps of metal on the earlier flywheel are too long for it to work well; the new version has a shorter bump. There is a box to give soft start to the green stripe modules, but it’s a waste of money if/when the old module dies.If the starter sense wire fails, that side will be stuck on 3 degrees ATDC with a huge power loss. Do you have the soft start add-on box?
Sadly, IDK what's happening with your engine since wire and module swapping still has "R" remaining the bad line. In your position, I'd start looking at the pulsed signals (trigger, plug wire) with an inductive pickup displayed on an oscilloscope.
