I ran into this problem a while back on a pro mod body. After trying all kinds of things I brushed some spare primer I had from working on my 1:1 on in a thick coat and wet sanded it until it was smooth.
Great looking paint jobs! was the flaked clear on the blue 56 chevy part of the "Paint Shop" line of paints that they sell at auto parts stores? (I think the cans have a 69 camaro on the side)