I like Geoff's idea, and I seem to recall the Doc saying you had access to a dyno. Might be worth an afternoon - optimize what you have, baseline the electronics and you'll have a starting point for the new cam, heads and rockers, and determine if it's the sensor.
You've got to burn up that leftover fuel in the tank, anyway, right?
And the Rev can re-learn the shift pattern.
PEEEEE NUTS - GIT CHORE PEEEEE NUTS