Well you definately need to re-map your computer... That will give the motor the capability to run at higher rpm's... But if yoour variator is restricted, then it isn't going to help a great deal... If the variator isn't capable of comming all the way together, then you won't be able to achieve your highest possible gear ratio. Without seeing the variator, I am reluctant to give youo advice to machining the shaft... I would just advise getting a new performance variator and re-mapping. The new variator will give you a little better acceleration than the stock would de-restricted any way. You are also going to want to lighten your roller weights. If you get the polini variator kit, it comes with 6.4 and 7.4 gram roller weights. Your stock weights are around 11.5 grams, which are way too heavy. I had really good luck with the 6.4 gram roller weights on my polini variator.
If you get the new variator and re-map your scoot, you should be able to get about 55MPH out of it with nice acceleration.