That #3 would have an occasional drop in vacuum has me confused. When you sync, or anybody does a sync, it has nothing really to do with spark or firing. All it really does is to adjust the throttle plates evenly so that each cylinder gets very close to exactly the same amount of air. It is then up to the carbs to deliver the right fuel mixture and the ignition system to boom it. So doing a sync at 3k can throw things off, for if a throttle plate was 10% of at idle it would only be off 2% at 3k (not scientific or real at all). The vacuum gauge is only used to judge the throttle plate position, that's all.
So now we have 1 cylinder, #3 that has an intermittent vacuum drop. For some reason, either the piston isn't drawing air, the intake valve is opening, you have a loose boot, there is a hole in the diaphram, or something, something is causing the lack of vacuum. I would chase that down first.
Are you sure you weren't pinching the vacuum line?
What sync tool are you using?