Think of the flow rate on a vacuum secondary Holley as being an "up to" number. That's why you can bolt a fairly large carb and still have smooth street performance. The carb will only flow as much air as the engine requires.
In the original post you pretty much identified the problem. A stock 2 barrel intake is like a restrictor plate. The primaries on that Holley will flow about the same as the mounting flange on that manifold. Grab a Performer intake off eBay and a lot of your problems will go away. But if you still have a stock cam and exhaust don't expect miracles
