i generally adjust my throttle cable first,,, back the idle adjustment screw all the way out, then adjust in the cable until i've got slack. then adjust it to where its only got the tiniest bit of slack,, start the bike and hold the throttle to where you want it to idle (i prefer a lower idle and will probably be told im messing my bike up by doing it that way or something). start turning in the idle adjustment knob until the rpm raises, turn it back out slowly until its where you want it. bump the throttle a couple times and make sure it goes back to the idle you wanted
I wouldnt mess with any of the jetting or anything until after you have everything else worked out for sure! The flywheel slack could have been what was causing your problems. go and fix that and it may be perfect now. but if you screw with the carb you wont know lol