If the bike was sitting for a couple of years without first draining the carbs, then the dried residue in the carbs may have plugged up the .016 inch slow jets wich provide fuel for idle operation.
Check the head pipes for temp differnces (flash touch) the cold ones probably have slow jet issues. At any rate this will tell you which cylinders are or aren't firing.
Another possibility is that the point contacts have oxidized. This would prevent two cylinders from firing (1-4 or 2-3). A point file or 600 grit paper should expose bare metal again. With the ignition on, you should read 0 volts across closed points and 10-11v across the open ones, assuming a fully charged battery. Check each set of points.
Cheers,