It really doesn't matter which one is the reference. You just want all 4 to be at the same vacuum. The Idle speed is automatically controlled by the ECU on 3rd gens. The only time you'd run into idle speed problems is if you cranked them all in too far or out too far.
I suspect that they paint the white dot on whichever cylinder has the lowest vacuum after they are all opened a predetermined amount (like 1/3 turn) or maybe when they are all closed fully. That way the other 3 can all just be opened up a little to match it.
What you suggest makes perfects sense but the stumble is not going away with the #1 screw any where from seated to 1/2 turn out and then the others re-synced accordingly. Several times the bike has run very smoothly for up to about 100 miles and is seemingly back to normal, only to start stumbling again. Yesterday I tried #1 at one turn out as suggested, reset the others and went for about 80 miles, and again, all seemed well until about the 40-50 mile mark and I started getting a very slight surge but not as bad as previous times.
The stumble was very slight so I'm going to live with it for a few more days and see. This issue makes no sense to me though. Why should it seem fine after initial sync and then the stumble creep in again? Been trying to figure if I've affected something else in the adjustment process, maybe fuel filter plugging up with all the tipping up and down of the tank? Bike has only 14k miles so this seems unlikely. Also ran some Techron through it in hopes maybe it was water in the system, also replaced the plugs, but no joy. Thanks for your input though, any thoughts are greatly appreciated.