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Well, assuming that all wiring is fine, according to the Suck, Squeeze, Bang, Blow theory. The next simplest idea would be fuel related. Check the specs on your injectors and ensure that they are in fact all in working order.
You said earlier that you noticed a change in performance when you moved wires. That tells me that it has to be electrical in nature. Do you notice it on one injector more than another? Can you manipulate the wires so that the miss goes away? Perhaps the wiring is shorting out or has a bad ground. Check and make sure the harness isn't rubbed through anywhere or anything obvious like that. Find the common ground and check and clean that as well.
I'm just trying to think of things that might cause it that wont cost a fortune to fix right now.
Hope it helps.
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"I've had my GSXR for 2 months and I've already topped it out in 6th gear. I'm bored of it and looking to move to a 1000."
-Proof that Darwin is still experimenting from his grave.
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