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It will bolt up to the motor however the output shaft will be 30mm further out to the left the 6 speed is also much shorter than the five, if you are happy to go down the custom swingarm or perhaps a V11 swing arm you may be able to do it. I would also look into what it does to the gearing I understand the 6 speed runs a different primary ratio to the five the the final drive ratio is matched to it.You could do it there wouldn't be much EV left after you did, it will be cheaper to rebuild your five speed the EV might not have enough output to really take avantage of the extra overdirve that the six speed has.
My '04 EV makes a whine in top gear which I believe to be that pesky plastic bearing cage but I do not know for certain so I seldom use 5th.