Is my NTV's fuel system causing rough running?

My Honda NTV650 93 model is running rough at idle and at speed it has a lot of vibration from the engine. I have put some carb cleaner though the tank for three tanks of petrol and it has helped the pick-up of the engine. It used to have a real bad flat spot between 3500-6000rpm but that’s now gone, but the rough running is still there.
Ed Barnes, email   
 
The fact that the carb cleaner seems to have had a positive effect would indicate that the problem is in the fuel system somewhere, but carb cleaner within the fuel will not fully clean a carb, just remove some fuel residue that may be gumming up the works somewhere. You need to strip the carbs down and inspect and clean each component. When you reassemble them, get the carbs set up right for float heights and mixture settings. Those figures are in a workshop manual, either Honda original or Clymer/Haynes. You should also get the carbs balanced. While you’re giving it a service check the valve clearances because they can set up a misfire if they’ve closed right up.