If you suspect carbs then try to borrow 2 from a Rotax technician. Fit in place of yours and balance. If you do not disconnect throttle cable, only remove throttle arm from carbs this makes job more easy.
New carbs does not stop my roughness on my motor.
If you look at maint manual page 'Propeller shock load' that is what I might test next on my motor. It looks easy if I can make piston stopper part.
Grzeg