OK Keith, I'll give it a shot at explaining why I do it as I do. Any way one can accomplish the task with the desired results is fine with me, so lets just call this my OPINION through deductive reasoning, a dash of experimentation and a sprinkle of practice.
Certainly, you can adjust the mixture screws before you synch, however, it is not possible to adjust them correctly before you synch. You can only get them in the ballpark. The reason is that mixture screws do not control the mixture directly. Every range/operating stage in the carb is controlled by one thing. That is induction velocity.
Mid and upper range mixture is controlled by needle, slide position and jet size. It can be implemented to a small degree with the mixture screws, but that is not the purpose of the mixture screws.
At idle rpm 1000-1200, the mixture screws are effective and being applied in their intended operating range. I initially set mixture screws only if the mixtures at idle are so far out that I cannot maintain a 1000-1200 rpm idle with the idle control knob. If I have torn down a carb stack for cleaning, on reassembly, I will usually arbitrarily set the mixture screws in mid adjustment range so the engine will run at idle. Normal range is from 0 to 3 turns out (more or less) I just set 1 1/2 to start with.
I then synch the vacuums keeping the rpm exactly the same between each adjustment to vacuum. If rpm varies, then velocity will vary, and if velocity has varied, then venturi effect has changed and consequently fuel flow has changed. This makes it impossible to meter fuel flow with a mixture screw before vacuum is stabilized.
Also, it appears that the designed flow characteristics (stoichiometric ratio) of the Mikuni carbs is matched to the stock jetting when flow rates are between 8 in Hg and perhaps 16-18 in Hg. The higher ranges produce more fuel flow and give richer mixtures which will provide more power, until a ratio of aproximately 10-12:1 is reached. At that point, plugs will start fouling. SO........... I pick intake velocity/vacuum for an rpm and synch to that. Once a uniform vacuum level is set, then I finalize the mixture screw settings. I determine highest rpm just like everyone else, then I richen them up 1/4 turn or so. My reason for that is that on startup, if the idle mixtures are at the upper edge lean, it makes the engine a little bit more peaky to start. I dont like to have to use choke, because choke is excessively rich and constant choke use fouls plugs (my opinion again)
My bike is set up such that I do not need the choke at all. I can leave it for a week untouched, turn the pingel on, wait 15 seconds for the float bowls to top off and touch the starter button. It starts in less than 1 second, immediately idles at 1100 rpm and will take the throttle being snapped to wide open instantly. No hesitation, no pop, just perfect response.
Earl