Rain is often the cause of what you describe. HTleads are openly exposed to it and so can loose their capacity to transport the energy needed for a good spark. The diagnosis is often complicated when the bike, after some time, performs well again. Now the wires may be dry, but there could still be mineral residues that will act as parasites and in a next shower the problem may reoccur. So step one is to carefully clean the HTleads with some alcohol or a water displacer like WD-40. Another possible 'rain' cause could be a missing or damaged gasket under the points cover. (A mist of) Water will find its way in there and can cause misfiring. BTW, that water will also remove the grease from the cam exposing the breakerpoints heels to premature wear. The above inspections are very easy to do. Remember: 9 out of 10 carburetion problems turn out to be of electrical nature... Hence my hesitation to go into the carb section at this stage. In case water has managed to find its way into the carbs however, I'd start with simply draining the float bowls. It takes a tiny often hanging drop of water to mess up carburetion...
Some CB550K3 owners have reported problems with the vent tubes, transporting water mist into the float chambers. Shortening the tubes with an inch or two is the remedy.
