Hello Pete:
You can sync with three gauges but you will want to swap back and forth a few times to make sure all are within 2 CM within each other.
You right in that there are 6 ports for a reason. Even though there are only 3 balance adjusters, reading all six ports will tell you if there is something off in the throttle bodies. Either mechanically in the engine, or within the throttle bodies themselves. this can be due to a blockage in the idle circuit in those non-adjustable throats, or possibly the butterflies themselves can be bent or misaligned.
So check all six to make sure.
I happen to have two 4 port manometers, which allows me to check all 6 at one time.
Before you begin the carb sync, make sure of the following:
1: your fast idle cam is adjusted per the book, at least start with that measurement
2: If possible, take the carbs off and bench sync them with a fine wire first. This will dial them in fairly closely and will assist you with a less than lumpy idle.
3: It would be a good idea to adjust your idle mixture screws out around 3 to 3.5 turns out, then adjust with a infrared gun, or ColorTune plug. (Most on this forum suggest the ColorTune method.) There are some good YouTube videos on how to use that tool.
4: As you adjust your blance adjusters, make sure they are adjusted within the limits of the manual. Too far in, and the bike will not idle, too far out and the throttle linkage will bind. (I think it is no more than 4 turns out)
Keep us posted.
Todd.