Fiddling with the idle set screw wouldn't have any effect save at just idle speed... so I wonder if perhaps you have a leak and/or yer fuel air mix is off. marts1 may be right - but also check to see if yer choke is messin' with you, some of them are known to move around a bit while yer riding.
Check your head & base gaskets for an oily discoloration near them & check the torque on the head bolts, also check the intake manifold where the carb mounts & flange to the motor. Pull the plug and check it's coloration - it outa be a nice tan, not unlike coffee w/some cream in it. If it's black - yer too rich and need to adjust the clip on the needle by moving it "up" (away frm pointy end), if it's gray or white - yer too lean and ya need to move the clip down. "Stock" setting is usually 2nd slot down.
Once alla that is squared away if yer still havin' problems give us a shout