I'm going to assume you are dealing with a Buick Nail Head engine since you said it is a stock GM engine and that is the only engine that comes to mind with 401 cid. It really sounds like a booster problem. The car came with origional Power Vac brakes and I am not sure of the ability to directly change this with a modern power brake booster. I have heard of people getting faulty boosters off the shelf in rare occasions also. Did you install a new master cylinder or rebuild the old one. By this time you could be getting some leakage by the piston arm in the master cylinder.