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!