do you have the throttle cable adjusted correctly? did you turn the barrel adjusters all the way in, then insert and clamp the wire? if not, you need to adjust it that way. otherwise, here's something to think about. a tomos base gasket only fits on one way correctly, yet there are 4 different ways it sits on the block and looks correct. so, when you assembled the cylinder, did you study the gasket closely to see how it fits? and did you use any type of sealer on the gasket when assembling the cylinder? and are the head bolts torqued to 10 ft/lbs?
all these things will cause idle problems.