Sounds interesting. If you can perform a gear change based on simple digital outputs then I don't see any reason why an Arduino couldn't control it. Do you have to do a power cut and synchronise the change with the fall in engine revs (like Zeroshift) or can you just slam it into the next gear?
A few years ago I used a clutch-operated rev limiter to support full throttle gear shifts but I could never convince myself to trust my engine to it so it hardly saw any use in the end. That's the problem with this sort of project - you really have to trust it, because if anything goes wrong then things could get nasty in a hurry.