You'll have to have a play and see what works best. Mine had 2 rather small holes in so I just made them bigger. Obviously one either side but apart from that there are no rules.
Steve and I did have a bit of a chat about this at the oh so well attended 2nd dyno day, he dropped about a horse going from 4 to 6 1" holes so he just taped them up. When I was down there the other week he had some 1/2 covered so he'd been playing again.
Andy also had a totally blank airbox lid (i.e. no inlet holes at all) which we were going to try a few different configs but we ran out of time.
And check the jetting. I can't really emphasize this enough.
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