In my experience, you really should use the HRC (or equivalent) jet kit, to get the most out of the modifications. It's extremely difficult to jet them and produce good power with a standard airbox, and almost impossible to get the NSR to carburet cleanly without the adjustable needles and HRC air correction parts.
As the genuine HRC kit is virtually impossible to find now, I would suggest a jet kit from T2Racing in Japan. I expect, although cannot guarantee, T2Racing could both supply you with a jet kit, and arrange re-coding of your PGM-IV & card. Definitely worth asking.
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Andy.
NSR-WORLD.COM
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