Hello,
Well wide open rpms with out your giving it gas usually indicates a air leak somewhere. i would double check all your fittings and boots by the carburators and the reeds.
On the fact that it only runs on one cylinder, does the other cylinder kick in after it warms up? If so you could have low compression on the one side. Speaking of compression, have you tested the compression on the engine on both sides ? What is the bike jetted at? What color are your spark plugs ? Also the knobs on top of the tors is the idle screws. Make sure the screws on idle are set the same amount of turns out. Did you make sure the carb slides are in correctly if you took them out? It is easy to accidently put the slides in backwards. Alos make sure the carbs are synched up. Make sure the throttle cable isnt binding anywhere thus causing it to stick open. Liek i said wide open sounds liek an air leak somewhere...find it before you have to rebuild
Also what mods do you have? You should list all mods, it may help diagnose the situation. You may want to look into purchasing a copy of the Clymers shop manual. Its the bible so to speak. It will show you how to tighten and loosen every nut and bolt on the bike, including engine overhaul.
Hoped I helped a lil...
~Nick