Yes it does. After rereading your initial post is this how the ignition wiring is configured? ignition circuit A: 1-2 TOP 3-4 BOTTOM. ignition circuit B: 1-2 BOTTOM 3-4 TOP
Are you checking each ignition circuit at 4000 rpm?
As a final check to verify the carbs are balanced have you pinched off the rubber hose on the balance tube and verified they are balanced? There should be no noticeable change in engine speed or vibration if the carbs are perfectly balanced.