Same thing happened on my QT. It ran the first day that I got it and then the spark was intermittent. I tried everything and eventually traced it to a fault in the charge coil under the flywheel (its the white one). I got the replacement coil ($30) and the flywheel puller ($20) from scootertherapy.com.
My flywheel was on so tight though that the puller actually pulled through the threads on the flywheel. So I went down to NAPA and borrowed one of their 5 ton pullers. It took a bit of doing to get it to fit, but once it did, that and my impact wrench ($20 @ Walmart) took it right off. I also used it to take the original flywheel bolt off.
Anyway... I'd replace the coil. Thats what everyone told me at the time. One thing mine did... if you let it sit for about a week, you could get a slightly more regular spark for about 2 minutes. It was never enough to maintain combustion... but you could check for that.
Hope that helps!