Rough on run-up

Carbs needs an inspection.Check the weight of carburetor Floats not more than 7 grams per set. The carb sync should be fairly easy to set dead on. You may have an air leak on the air intake carb rubber flange or even where the air intake screws onto the top of the head. Just double check the mixture screw on the neck of the carb for 1.5 turns out.
and check the spark plug Gap should be between .023 - .027. It's in the Line Maint.

visit here please

http://www.vliegclubmoorsele.be/docs/Rotax912Troubleshoots.pdf

I suggest open the carburetor (first Left side then Right side) change the mixing tube with jet change one by one and start the engine.do the carburetor synchronize and  start the engine.

Were the Carbs Touched during the "Inspection" ?  Not Rebuilt!

If the Floats and Sync have already been checked, have a peek at the Spark plugs just to give a hint at where to look next.

Let us know what they look like.

Is this just a Mag-Check issue?

How does it run under power?

EGT Temps changed ???

Put the needles back on the 3rd notch, your mag drop will improve and the roughness will go away.

I have replaced the floats in both carbs with pairs that weigh 6gm each. The needles are on the second notch from the top and I synced the carbs using a Carb Mate pneumatic tool. Low speed (under 3000 rpm) is smooth, but when I dial in throttle above 3000, the engine surges, with the rpm varying over 100 rpm with no additinal throttle input. 

It is summer in the Pacific Northwest, and we have a rare stretch of sunny weather. The floats on my plane are drying out and need to find a lake soon. Time ont the engine is around 300 hours.  

What is the next step I should take?