This is just a word of wisdom from someone who's been there and done that and got the tee shirt. I'd be real careful about taking it for an extended ride when the bike is running on one cylinder, especially if you have a suspected crud-in-the-carb problem.
Take it easy on this ride and if the other cylinder begins firing just keep taking it easy for the first several days afterward to give the fuel system plenty of time to clear its arteries.
If you don't you could suffer my fate from awhile back. I thought everything was hunky dory and took my bike to the drag strip to practice a few launches (in anticipation of an upcoming race weekend). Mid-way through the 2nd run the rear piston "detonated".
It turns out that if the cylinder running way lean (because the carb still isn't completely cleaned out or other issue) the piston head can get overheated. The incoming spray of fuel/air from the intake helps cool the piston head.
Here's how my piston looked when I dug down to it. The shiny round places are where chunks of piston head blew off. You're looking at the piston rings. Fortunately the pieces of piston made it out the exhaust port without doing further damage (other than to un-gap my spark plug).
