So do any of the Gray Fox theories have any basis at all?
Not really. A CG test and a picture from a motion capture
might be hinting at Gray Fox being in the game (and it would make sense for him to be around, timeline-wise), but the picture is that of a man holding what looks like a sword, i.e. classic Cyborg Ninja/Null stuff. The connection to Punished Snake is a bit of a stretch, at this point.
I'd honestly like to know if I'm missing any hard evidence, or even any vague hint. that the Big Boss in Afghanistan is not the same one in Ground Zeroes
That, on the other hand...
1) In the scene where Big Boss is said to be in a coma, Kaz's "what about him?" hints at a third (unseen) wounded man being present.
2) We're seeing that scene from the third man's point of view. And when Punished Snake then wakes up (nine years later, apparently), we're seeing things from his perspective. Third man = Punished Snake?
3) Punished Snake has a piece of shrapnel in his skull. It's already there when the hospital is under attack (you can see it under the bandage). There's no piece of shrapnel in Big Boss's skull when he falls into a coma.
4) Punished Snake somehow still has his head bandaged after nine years of coma. Maybe that's from a wound sustained during the attack of the hospital (and that may also explain the sudden piece of shrapnel, but would the staff really have the time to deal with something like that in those circumstances?). Maybe that's from some other, recent procedure.
5) When the hospital is under attack, Punished Snake is helped by a mysterious man who calls himself "Ishmael". "Ishmael"' seems to have the same voice as Punished Snake (Kiefer Sutherland), his face is completely hidden by a bandage, he says at one point "I" but immediately corrects to "we", he points to Punished Snake when he's asked who he is, and he doesn't seem willing to offer much needed physical help. A theory is that "Ishmael" is a figment of Punished Snake's imagination. Could be because of that piece of shrapnel, could be because of that Psycho Mantis-looking boy, could be because Punished Snake has identity issues.
6) Kojima might be trying to reference
Metal Gear Solid's Fox Hound members once again (after the BB Corps in
Metal Gear Solid 4). Eli most likely is Liquid Snake. Ocelot obviously is Revolver Ocelot. Quiet is a female sniper like Sniper Wolf. Code Talker seems to be a native American shaman like Vulcan Raven. The floating boy with the gasmask might be a younger Psycho Mantis. All that's left is Decoy Octopus. Maybe Skull Face is filling that spot. Maybe Punished Snake is a Big Boss decoy.
O (and his role in it) is in fact cannon.