Tyger, not sure if you have much experience with Rotax two strokes.
Even the four strokes will shake and rattle if the idle is set too low, but the two strokes do it very badly if the idle is too low.
Generally, about 2000 rpm is where the engine and gearbox and prop smooth out. In some set up's you it will run smooth a little lower than 2K and in others it will need to be a little higher than 2K, but regardless.... You need to always try to keep the engine idle speed high enough that it runs smoothly and no shaking or rattles.
On my aircraft, I will NOT set the idle on the carbs high enough to run smoothly. I Just advance the throttle lever forward enough to idle smoothly once the engine starts. I do this because once airborne, due to the air flowing through the prop, your " in air " idle speed will be a few hundred RPM higher than your static on ground rpm. So in the air you can pull the lever all the way back to idle and have a smooth idling engine.... If you set the RPM to 2000 or above on the ground, in air your idle will be perhaps 2500 or so and you will always have a little push of thrust even at idle. Not sure if that all makes sense the way I describe it... But for example its the same thing on my airplane... I have the idle set to like 500 rpm on my O-320 in my RV4, but on final as I am coming in to land, ill be showing 850-900 rpm. at 500 rpm the engine barely wants to run, so on the ground I keep the throttle lever slightly advanced. If I set the static rpm for say 750-800 rpm, the airplane is hard to get slowed down on final and will " Float " down the runway much further before its done flying.
The higher idle speed the two strokes need, is one of the reasons the RK-400 clutch is so popular. With the Clutch, the engine idles much lower rpm and idles smoothly with the prop sitting still. Advance the throttle and around 1800-2000 rpms the clutch engages and the prop starts spinning and everything stays smooth.
The fact that Davids gearbox sheared those three bolts, Means to me that someone has operated for ALOT of time at too low of a rpm. And a Rotax engine shaking and rattling at that low of a rpm shakes the crap out of the entire machine. I would look real hard at all the engine mounting hardware as well as the entire airframe for cracks and wear.