Let's break it down into smaller pieces.
First, trim the area in front of the battery box for improved Uni clearance. Don't actually cut the container that the battery sits in, just the plastic in front of it. Also, are you using a straight Uni or a 15 degree neck?
Second, the stock jets in the Mikuni probably won't work well. You need a 110 main and a 25 pilot. Have you changed the jets?
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Weldangrind
"I figure I'm well-prepared for coping with a bike that comes from the factory with unresolved issues and that rewards the self-reliant owner." - Buccaneer
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