Your description of the pistons leads me to assume they are not dished. It seems they are flat tops with dual intake valve reliefs. If so, then it is safe to assume the pistons have also been replaced.
Dual valve reliefs would indicate the pistons have close to OEM pin height (1.650"), and are probably either cast pistons or TRW forged pistons.
While the engine is apart this far be sure to replace the nuts on the connecting rod bolts, and make sure the valves have been replaced (no multi-groove style valves or intake valves having the Ford oval on the valve head). The final precaution is to replace the crankshaft damper with the Power Bond "Race Performance" damper #PB1082SS.
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