I would begin by familiarizing myself with what comes stock on a 2009 GT from the factory.
Parts beneath the hood that are not OEM colors, have names stamped on them other than "Ford" or "Mustang", or are obviously affixed to their positions with hardware that looks different from the rest.
Unfortunately, the OBD port is not going to jump up and say, "I saw the whole thing!". The most it will tell you is whether or not it has been altered itself.