Yes, I ran a vm18 and bored out my stock intake. A lot of people on here beg to differ, but that carb setup worked perfectly. MLM makes an intake now for the qt50 that would work a lot better. Mine was the first bike on here built with a malossi kit, and to this day the cylinder hasn't been off. A lot of miles on it and still shedding 53-54 mph while still holding a crazy mid range power band that gives you a smile from ear to ear.
Back when we were building a handful of malossi qt50's I tried to run one with the stock exhaust to break it in. The bike ran terrible, thats why I think you have an exhaust issue. A friend of mine had a one piece bi-turbo from a 95' tomos. I cut off the header and turned it slightly, also when I had the header off I slid on a new flange i made out of 3/16" steel. Worked perfect and Honestly besides the Jemco pipe its the best we've ran on the malossi cylinder. Also I strongly recommend a vm18. If you need a shim made to use the stock intake PM me.