Re: metering rods
The flapper's there to prevent too much air getting in until the secondary vacuum's high enough to suck the fuel out of the secondary jets (the vacuum below the flapper that does the pulling. And also there's the delay in the fuel getting up there - it's much heavier than air, so it doesn't get started as fast. It's the same reason an accelerator pump is needed.
If it opens too early, the engine goes lean for an instant. It can be adjusted easier or tighter, depending on how you turn the screw - or bend the linkage.
The complaint wasn't a bog off the line, nor was it after the secondaries opened, it was during the transition. Either the secodaries accelerator pump isn't working (as on a Holley Double) or the flappers not doing it's job.
Try it without the flapper - bog city!
Yes, slight changes are needed due to velocity changes, and the "gulping effect" of more "gulp" by the cam. But stochiometric is still stochiometric.
Increasing VE changes the total amount of the mixture needed each "gulp" but does not change the balance - ratio between air and fuel.
Yes, different engines often use different jets - not appreciably different though. Notice often the larger engines use SMALLER jets than the smaller engines - or larger metering rods, or a combination thereof. Partly due to the fact the venturi velocity is higher because of the greater total volume, making better atomization.
The reason that a big cam usually gets larger jets is because the idle and tranfer circuits are really affected by the huge gulps. Because of the high velocity during a gulp, the carb switches from idle, to intermediate, then to main run, then when the gulp stops, the main run spills over - but the engine can't use it because there's no Oxygen to go with it, the carb drops back down to the idle circuit just about the same time the next gulp hits. The next guylp lots of air gets in without any fuel due to the heaviness of the fuel. Over and over again. Poor carb just doesn't have a chance.
There are ways to minimize it depending on the carb. But the usual method is go big jets and a high idle - it's easier.
Once throttle's open and the velocity gets more even, the mixture still needs to be just slightly richer than stochiometric.