I once had a somewhat similar issue when I overfilled my tank (I have Cali emissions stuff on my bike). That is to say that when the cold fuel warmed up and expanded after a fill up, some fuel worked it's way into the california emissions stuff, and really messed up how the bike was running. As I remember, I detached the vacuum lines and used my lips/lungs to blow some air through the line, in an attempt to 'clear' the liquid blockage. This seemed to help, and once the charcoal cannister had a chance to evaporate the fuel/dry out, it was running fine again. The moral of this story I suppose (if you have Cali emissions) is to not fill your tank all the way to the cap/overflow, especially on hot days.
Some people have removed the Cali emissions stuff (and most Connies don't have this stuff to begin with) as it isn't really needed at all, but if you live in California the State might get upset with you...
So if your bike is running fine now, chalk it up to the emissions hardware getting temporarily gummed up. Also, the comments about sediments above could be valid if you are still having issues. I had a piece of debris partially block one of my float needles once, and by using the 'on/prime' position on my tank petcock while opening the drain screws on each float bowl to quickly flush each bowl, I was able to flush this little bit of blockage away. Of course, if you have debris in your carbs (I suggest draining into a cup, using a length of hose to attach to the nipples at the bottom of each float bowl as you open it, that way you can see what gets flushed out besides fuel), this might be a good excuse to clean/rebuild your carbs, or even better, ship them to Steve at
Shoodaben so he can install some overflow tubes and give you some better/more efficient jets.