With later heads the engine may have been previously "built" and the bores not at standard values. Depending on your intentions a simple rebuild should use the 396 specs for the short block and the head specs for the numbers on the heads. Start by getting a Chiltons book but I'll bet any specific question you have will be answered here by experts. In fact if you mic the bores, measure the diameter of the valves and include the block and head numbers in a reply you can get more specific advise here.

Don Shillady
Retired Scientist/teen rodder