Here is what I would try: first, check everything else out to make sure nothing else is contributing to your troubles (valve lash, point gap, timing); next, try spraying silicone spray around your intake manifolds to make sure you're not dealing with a vacuum leak(s); if none of that finds anything, you need to set your idle the old fashioned way.
Unplug the right hand cylinder and start the bike (if that doesn't work, get the bike running and use insulated pliers to unplug the cylinder while throttling to keep it running). Adjust your idle screw on the left carb (on the ends of the small arms on the outside of the carbs) until the bike will idle around 800 to 1200 rpm. Now unplug the left and do the same for the right side. Now plug them both in (it will idle around 3000 or so) and adjust both sides evenly until the idle is around 800 to 1200. If you still have a climbing idle, check both exhausts for even output. If they aren't even, adjust float height and mixture screws as needed until they are even and reset your idle.
I hope that's helpful for you.