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well i have a manual for the 03-04 that i use for my 06. my book says 2 blinks is MAP(mass air pressure) sensor performance problem. the cause: loose or poor connection on MAP sensor vacuum hose.
I had the same issue when i put in a new filter cause i took the bottom part of the air box out to hook up a power commander at the same time and when i did that it was a small vacuum line in the rear part(close to the seat) of the air box on the bottom that i didnt know came unhooked. my bike would barely run with out it.
not sure if that will help you being you have a 07 but its worth a try.
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ya man it was the same thing except i couldnt get it hooked up so i rerouted over the fuel rail not thinking that it would get pinched tight so i rerouted that again and turned the key and ran like a top again. thanks man!