The filter is in good shape, I had it out at the end of last season to check it. I didn't stop along the road and pull the plugs, but if nothing else checks out, I'll take a look. I'll also take a look a the vent hoses and see if I can find anything out of place. Everything is where it's suppose to be, best I can tell. It ran like a beast north and south, but the air blowing in the left side created havoc.
Perhaps no direct bearing on your current issue. But, the stock filter will not last indefinitely. With use, it gets more and more restrictive as it traps particles that just can't be cleared with the compressed air blast normally used for cleaning. The maintenance schedule for the filter is clean at 3000 miles of use and replace at 6000 miles of use for this reason. A very dirty air filter is easy to observe, but a restrictive filter is much less obvious. I put a strong light on the inside of both a used and new filter which made it more obvious that although cleaned, the used one still had more discoloration and was significantly darker than the new one.
How could a restrictive filter cause your problem? Well, gas will ignite when mixed with air in ratios of 10:1 to 20:1, with 14.7:1 being ideal in a perfect engine. If we assume this is what is provided with a new filter, then as the filter becomes more restrictive, the ratio increases. At some point, there will be too much fuel to sustain combustion.
The carburetors are effected by barometric pressure, too. High and low pressure weather patterns effect mixture delivery. Crosswinds can effect barometric pressure in microclimates (also called turbulence) around various parts of the motorcycle. When this occurs at your carb vent inlets or the air filter inlet, fuel delivery mixtures are effected and may exceed the range that can support combustion and may be exacerbated by a restrictive air filter.
The hoses can be plugged up by insects making homes in the tubes. Some plug the ends with mud. Others crawl in and spin a nest from their own secretions. What ever you do, don't blow crud into the ends of your carburetor vent tubes, unless you enjoy cleaning carburetor innards. Disconnect each one and blow from the carb end.
Was the cut out you experience coupled with some engine burbling, or was it more like a wheeze or as though the ignition was temporarily cut?
Cheers,