I am happy to report that this process has resulted in the vacuum on all 3 throttle bodies being in sync. Once I understood how the valves sync via the linkage, and had visually seen that the ones on my bike were not closing simultaneously, I had no qualms about giving it a try.
However there is one minor hitch in my case: After syncing the butterfly valves, the bike idles too low, around 850, even with the idle adjustment screw turned all the way in. There is no more increase available and the engine is prone to stall. I have listened to the TPS, and it clicks as recommended, just on and off of fully closed throttle.
If I were to re-sync the Idle Air Bypass screws with my homemade device and open them up more, allowing more air in, will that increase the idle speed? I think I may have made a mistake when I didn't open them up the recommended 1 1/2 turns to start the adjustment. After adjusting the butterfly valves at 2,000RPM with the bypass screws closed, when I reduced the throttle, it was close to being in sync then, and I only opened up the bypass screws enough to sync them. Oddly enough it idled at 1,000RPM. At that time though, it had been sitting still and running at 2,000RPM while I adjusted the butterfly valves, so that may have affected the idle at that time.