Ww had an old Honda CL450 that did this too. The problem as far as I could tell was the slide blowing open at low RPMs. They're a diaphragm type slide, so they're pressure controlled instead of being connected directly to the throttle cable. It's hard to pinpoint why it does this, but I'd check to see if you have even compression and check for air leaks. Also, check to see that the diaphragms are in there properly and that the slide is moving freely.
Another thing to check is to make sure that the cable isn't hanging up at the splitter junction (considering it has one.)
1985 Yamaha YTM225DX
2014 Yamaha WR450F
2008 Yamaha TW200
1975 Honda CB400F