I think you may have manyvariables here, so pick on e and start there....
timing...stock curve? vac advance? what vac readings are you getting? (should be nearly 14 in at idle at maniold.) is vac advnace plumbed in correctly? (shoud go to a carb port)

Jetting? any clue where you are or where to be or if you are close now?

Manual sec'y on carbs?
Auto or manual trans? Generally manual sec'y are for maul trans, vac sen on auto...but you can make it work either way.

Are your primaries set to open together, or progressively? if together, then you'll need 2 vacuum guages, one for each carb. you'll adjust the throttle plates so that both carbs pull equal vac. then you can set up the other linkages. - equal vac menas both are working evenly, and that is what you want.
if the linkage is progressive (the way trip 2bbls work) then it is kinda up to you as to what you want.

Since Ford and Chrysler both made dual quad factory engines, you could dig up the carb adjusting procedures for one of them and see what you can apply to your situation.

I have read about setting up dual carb VWs/Corvairs, and have 10 years with motorcycles as a pro mechanic (mult cab is common, but two stage is not).

Hope i have helped some....