1. Raiden DID have a replacement jaw in MGS4.
2. The idea of it being Gray Fox because of the eye that was shot out by REX in MGS1 and the mystery character wearing an eyepatch over the same eye insinuates that the game takes place after MGS1 in which Gray Fox died. Though it's worth pointing out that this wouldn't be the first time that Gray Fox's death had been retconed.
3. We never got sight of Raiden's upper forehead through his helmet and hair. He could have very well had the screws.
4. The only real inconsistencies are the barcode on the forehead and the different color eyes. I don't think barcode is a valid inconsistency since I see no reason why it couldn't be removed and once again it wouldn't be the first time the color of one of the main character's eyes was retconed, not that it would have to be to even explain the difference.
One thing that supports the idea of it being Raiden is that MGS4 quite clearly built up and eluded to a story behind Raiden's change. For one we aren't provided with exactly how Raiden went about his change or the exact story behind it. Secondly, Kojima apparently decided to retcon the death of Dr. Madnar who died in the 1990 game Metal Gear 2 and provided absolutely no reason or explanation behind it.
