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*How recently did you replace your plus and wires? Did this show up soon after?
*How recently did you sync. carbs? Did this show up soon after?
*How old is the gearbox?
Are you leaking fuel at any of the carbs? Check for stains, Rotax had an issue with some of their floats and it can cause it to run rough at lower RPM, there's info on the internet on the problem.
How does the engine run during Carburetor Synchronization ? Is the compensation tube back to normal and connected ? I would do the carb sync from scratch and make sure the idle screws are set correctly to start with. When doing a run-up do you get about the same RPM drop when each ign sw is turned off ? I'm assuming you don't have an engine that falls into the group that has carb float problems as per a recent Service Bulletin.
Search for your problem on the Rotax Owner Forum. I think you can search the forum even if you're not a member. If you're not a member I would suggest you join since they also have some good videos on maintenance.
Is one/both of the chokes sticking open or partial open?
They only work when at idle...
Check 4 top plugs for color and determine whether one side runs rich or lean. Plug insulator should be tan color. If one side is ok and other sooty, choke may be open on rich side.
Next, balance carbs at ~1800 rpm so engine runs smoothly. Engine operates at idle and close to full throttle, with mid-range ops just during landing. If it's balanced at idle, should be good for all rpm.
Plug gap should be ~.025".
Check cables on choke to assure they open fully for startup and close fully after start. Had friend with this issue and short cable was the problem.
If you do these checks and want to contact me offline, I'm at <email@example.com>