U can buy a kev fuel mod, or can make one for urself to solve the problem.
and yes the stage 1 replace the stock filter inside the airbox!

http://www.off-the-road.de/en/DNA-St...earchparam=dna

http://www.off-the-road.de/en/XT-660...earchparam=dna

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XT660X '05 - BIG BORE 102MM - PORTED HEAD - CP TECH PISTON 11,5:1 - PC III - AKRAPOVIC EXHAUST - HOMEMADE DNA STAGE 3 - CRD HEADERS - THROTTLE BODY +2mm