Re shot peening the rods can do more damage than good. Ford has a specification , air pressure ,shot size , time being blasted , to get the desired surface hardness, Without that knowledge , there could be an issue.
As others have already said "costs" have to be looked at and that usually has the aftermarket rod being a better choice , both cost and durability wise. It's real easy to dump too much money into stock rods and still have a weaker part in the end. The least expensive H beam rod is superior to the low riser rods simply by design.
Randy