One size doesn't fit all
This is why I always try to buy Ford Racing/Motorsport replacemnet parts for routine items, like a radiator. Decent quality and no fitment problems.
I would call or go back to the Pep Boys store and have them double check the part numbers on the radiator you have. Some clueless clerk could have put in the wrong info and sold you the incorrect radiator for your 'Stang.
Those pads shouldn't be removed and the stock brackets should fit, at least they did on my Ford Motorsport 3-row radiator, but that was from Ford or at least built to Ford specs.
They may have sold you a 'universal' 3-row radiator.
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