Jas the Ace

Plastic cups over the air filter, Hmmm, i honestly don't know why manufacturers put them on for!! My guess is so the air filter stays in prime condition in transit etc.
But Motoman I would certainly advise to run the engine without this on hey. You want the maximum available unrestricted air flow possible, otherwise you are basically "choking" the engine. The more the throttle opens, the more fuel is being allowed in, and if it can't get enough air into the mix it is naturally rich.
I am not saying this will solve any problems you may be experiencing, but it is well worth a go and see what happens. But hey once you have it tuned and run in properly you are going to have a lot of fun with it and you will soon forget about the painful run in period.