I've never worked on your year bike. but here's my guess. that black box controls the timing, it only uses those sensors as inputs for what timing is needed. I've never heard of resetting one. in fact I always thought when they go bad, they just stop working and the bike doesn't run.
don't reading any of this thinking I know what I'm talking about. because I don't. but can't hurt to throw my guess out there.
let us know what it was when you get it fixed. so I can see if my guess is right.
but as bamf said. has anything been done to the bike, like changes to the air box? or some of the older bikes have rubber tubes from the air box to vents somewhere. I rode a hacked up zx9 once that was fucked up. after the owner put two rubber air horn looking things back in. it cleared right up and hauled ass.
anyways.. if all else fails, a good shop with a dyno that logs air/fuel and can tune carbs should be able to figure out what's wrong.
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