Manifold or timed vacuum spark is a question the answer to which depends on what state of tune the engine is in.
They will run with either, but engines with long overlap and shaky idle quality tend to be "quieter" at idle with timed spark.
I think you may have overlooked some internal passage in the Holley which allow vacuum to find the blanked throttle, such as the idle and transition ports in the wall adjacent to the throttle disc. Have you tried closing the dead primary from above?
BTW: a 600 has all four throttle discs the same size, but the primary contribution is less than half because its venturi is smaller and the booster occupies some of the area. You have perhaps 76-78% of 600.
