All done,

Tom, the engine it's been opened for inspection two weeks ago. My mechanic was suspecting of a valve issue so he dismantled the cyl heads & body to inspect everything down to the engine block (including a visual inspection of the camshaft). Everything was within tolerances as per manual, including the reduction gear on the press bench, the cranckshaft eccentricity and the cyl. compressions. There was no founds to explain such a vibration. So initially it's not a mechanical reason.

The ignition cable is check on both ends (plug adaptor/dual coil) by checking the length of cable wich fits in and the pull test is done. Ignition cables are new, plug adapters are new ... Every time cutting a small piece of cable to ensure it will screw in properly. Ignition components have been check for resistance with multimeter on several occasions and all values are correct as per rotax manual (stator, grounds, dual coils, ignition cables and plug connectors).
The plug wiring order is been check as well and it's correct.

Since all this was checked with the engine stopped ... It might be a failure that it can be only reproduced with the engine running?

Main ignition switches. I didn't replace those but I bypassed them by directly connecting a cable to ground the CDI's to the airframe. Is that what you meant?

Another stupid thought of mine ... I tried by isolating the engine from the airframe by doing separate fuel and grounding to the CDI's. The only thing left that comes to my mind, is the power to the starter motor. Maybe it gets stuck or activated while the engine is running making some kind of interference? Anyone had any issue with this? I guess in such case my starter would had given up long time ago but ...

Thanks for all your comments, highly appreciate them!
Jorge