In my experience with all the carb'd bikes I have owned or worked on, synchronizing the carb with mercury sticks (Motion Pro) was the only way to visualize and confirm if the multi bank carbs has any chance with respect to vacuum to be eliminated out of the equation. And to answer this question, YES I have numerous times where my '95 900RR will not idle because the synch was way off. Even when completely removing the carbs and working on them, I found that even tightening them back on, the rubber boots were not perfectly sealed as before and you end up chasing your tail every time the carb has to be removed. I believe the fruits of your labor is going to be confirming and dialing in the vacuum to within acceptable limits for your carbs. When you get the hoses installed into your intakes and everything is ready, you're going to instantly hear the behavior of your bike when adjusting the synch screws AND seeing the actual measuring on what that is with the type of gauge you use.
I do agree you have to initially adjust the idle knob on the bike just to get it to rev continuously higher when you're synching but not so much that you could accidently suck mercury into the engine. The RPM will also not stay there and will go up or down accordingly when you start your tuning.
What Motion Pro does not teach you is if you can get to this point, adjust carb 1 to 2 (left screw). Don't care what carb 3 and 4 is reading. They will be way off from one another but don't fret. Then synch carb 3 to 4 (right screw) until the delta between those two are within 0.25" of Hg of each other. Now bare in mind 1 and 2 are synch'd ( <0.25" Hg) and now 3 and 4 are synch'd (<0.25" of Hg) BUT 1 and 2 could be reading 10" of Hg and 3 and 4 could be 15" of Hg. Now for the money shot, synch all banks together (middle screw) to get all carbs to within 0.25" of Hg. Basically remember outside-in. Don't adjust the middle until the left and right are good. If you synch middle first and then left or right screw...from my experience you end up again chasing your tail and takes longer to synch.
Remember, when doing this, you may need to tweek the idle knob just to synch at a RPM that you want to tune the bike at. Also lightly blip the throttle several times when you think you have the adjustment where you want it, to see the behavior.
All good points from above and my suggestion is while separating each individual bank and complete cleaning has its merit, try synching with a tool first before doing this because I don't think you're wasting your time or money investing in a carb synch because I think you needed this anyways. I wish I was in your position, because like you said, the wealth of info you obtain when you determine root cause whether it was mechanical (valve adjustment...yes I did this with shims under bucket style), fuel (filter, pump, jets), air (boots, dirt), or electrical (battery, coils) you can pass this down to all of us.