It is unlikely that the CDI is the problem. All anecdotal evidence indicates that they fail completely when things go wrong. Pin 2 is something of a mystery, but speculation is that it changes the timing ever so slightly when starting the bike, but it "should" have no effect once the bike is running, so your resistance checks on all the other pins would indicate that the CDI wouldn't be the problematic component.
You could probably rig up something to check the consistency of your spark on each cylinder, but I'm not sure how visually accurate something like a timing light would be if you think it's just missing every couple sparks. Something like an oscilloscope would for sure do the trick, but that's not something you find under most workbenches!
That’s interesting, would the standard Oscope probe end handle that spark? I have a scope from when I graduated electronics tech school back in the mid-90’s. The school was refreshing their equipment so they sold off their existing stuff. I landed a job/career in telecom engineering so the need for component level testing went away long long ago and it’s been shelf bound ever since.