Yes, increasing the main jet effects highway cruise (approx 60 mph plus) and also wide open throttle. It continues to feed when the power valve opens, The power valve is allows additional enrichment to the main circuit through the PVCR.

If the main jets are much bigger than the idle restrictions (they usually are) they will not effect idle-transition circuit.

The accelerator pumps are there to cover the delay in fuel responding to the throttles opening suddenly. Get the main jets based on cruise. Get the main jets + PVCR based on 3rd or 4th gear run at WOT. Accelerator pumps usually are most needed at when the throttle starts nearly closed. The main circuits respond pretty quick to throttle changes an often need little or no AP shot.
Pick up a copy of Ulrich and Fisher's Holley Carburator and Manifolds book if don't have a copy already.