The latest information I have heard from a long time SC enthusiast directly from a Ford engineer involved with the SC, is that those pins are in there for final engine balance and do not balance the damper and pulley as a unit. Therefore, the pins should not be removed for your new pulley, since it and the old pulley were already neutrally balanced.
The pins are located in holes around the outer ring of the stock damper and would be seen between the engine block and damper (if you can see back there, lol). Not all balancers have them.