I have a Kewlmetal Air box...Hindle exhaust...and a Juice Box. Hindle went on about 2500 miles ago. VERY rough running when accelerating at around 3500 to 4000 rpms..or around 50-60 then it smooths out. Hesitates in that range....kind of sputters....answers?
It sounds like a mixture issue at that RPM range. Either running lean or rich, I would guess lean. The old Aprilia tune for the V990 engine was lean between 4000 and 4500 RPMs. It may be worth a trip to a dyno to see what the mixture is doing.
Don't be afraid to run the RPM high on the Rotax engine. It loves to rev and is just starting to sing at 5000 RPMs.