Assuming you have the Nikki 2-barrel carburetor, I'd say the idle transfer passage is stopped up on the side which will not idle on one cylinder. This passage is TINY and must be 100% clean for the engine to run properly.
Did you completely disassemble the carburetor to clean it, or just drop the bowl and spray it out best you could?
To get the idle passage clean, you'll need to remove the carburetor from the engine and take the bowl off. Remove the two screws holding the plastic main jet holder to the carburetor body, and remove the holder altogether. Now, turn the carb over and remove the metal cover (held on with 3 screws) for the idle passages on the top of the carburetor. With this cover off, hold the carb up to the light and look up from the float chamber through the two small holes (one on each side) which feed fuel up to the top of the carb. Both holes must let an equal amount of light through. I bet one is partially- or completely-clogged.
These clogged idle passages are the reason why so many people struggle to clean and rebuild these V-twin carburetors. This carb can be built, but most guys get frustrated with them and can't figure them out, so they just buy a new one. I say give it a thorough cleaning and possibly a 797890 kit and see what happens.