Large RPM drop during runup

Try replacing your plug caps. Don't forget to cut 3/8" off the end of the plug wire, add a tiny dab of dielectric grease, and screw the caps all the way down.

Please check out these videos:

https://www.rotax-owner.com/en/videos-topmenu/free-videos/695-Rotax-lockwood-ignition-troubleshooting

https://www.rotax-owner.com/en/videos-topmenu/free-videos/708-rotax-lockwood-easy-start

I tried the connector swap thing. Swapping either connector makes the issue switch sides in terms of which switch causes problems. I think that means the problem is "downstream" of the CDI modules, pointing to coils/wire/spark plugs. I've had inconsistent results from the choke test but usually there is no change when pulling the choke.

At one point on Monday, while I was doing the ground run where the engine was gradually improving, I recall having the issue seem to "switch sides" unprompted. Not sure what's up with that.

This engine does have the new easy-start modules. I'll double check the integrity of those wires next time I'm out there.

Had similar issues caused by thermal paste. Thought I was using it sparingly but a small amount in the wrong place causes major issues.

Have you checked the trigger coil gaps on the back of the engine. 300 rpm is closer to one plug issue. A 1000 rpm drop is not 1 plug. I'd be looking at wiring to the ignition modules and at the 6 pin connectors.