what 2 cylinders?
1&2? 3&4? fuel getting starved.... maybe fuel kink, maybe the float height is messed up and your starving the carbs
1&4? 2&3? points dyna electrical problem....
check the plugs? anything wierd
What 2 cyls? That's hard to tell when the headers of 2 cyls that aren't firing at that time are still smokin hot to the touch from when they were firing a moment before and by the time I get home it's back to running on all 4 again.

Highly doubt it's fuel related because there is no power loss or surging leading up to it, it literally happens as if being switched on or off which is why I suspect faulty wiring or a failing dyna and it's rapidly occurring more often and lasting longer.
As it stands now today I was able to find another advancer from a 750 in a box of parts, I removed it's points cam and put it back on the advancer of the 550, put points plates back in, set the point gap, set timing, fired it up and took it for a LONG ride and the bike never missed a beat the entire time. On the other hand with the old dyna I was lucky to get 3 miles down the road the last time I rode it before it started loosing 2 cyls. I was trying to do a process of elimination so other than swap the points back in, no other changes were made, I even left the factory '80s Kaw 3ohm coils that it's using in place.
Does that mean it's fixed now? Sure seems that way at the moment but I'll need a few more long rides and it not missing a beat in the process to confirm it but before I do I'll be swapping the factory 5ohm coils back in tomorrow before the 3ohm coils smoke the points.