I went to buy a filter for the Mustang today, and found that the Cobra's took a different filter (all brands had a different part number).
This didn't make much sense to me, and out of curiousity I figured I would ask. I always assumed the Cobra had the same block, and the minor HP differneces were changes in heads/intake/cam stuff. My only guess is the Cobra may have a factory oil cooler, and due to clearances, requires a smaller oil filter. This is just a wild guess (though for my car, the oil filter is the same with or without the factory oil cooler).
Doesn't really matter to me, just figured I'd expand my knowledge base a tad.