I think (without being there, of course) you are fighting different issues at the same time and trying to solve it with one course of tuning. Get your primaries in sync and working flawlessly first. I'd disconnect the back secondary linkage on both carbs and focus on primaries only. Get it to work on both primaries at idle, part throttle, and sudden mash to the floor. Then introduce the rears by hooking up the secondaries. I've done this before (not on dual quads) to sort out one issue at a time.
