1. MGS3 is the story of the people that would become the original Patriots(Major Zero, Naked Snake, Ocelot, Eva(Big Mama)). Naked Snake, your character in MGS3 goes on to become Big Boss, who is the old man talking to Snake in the graveyard in the end of MGS4. Major Zero is the old guy dying in the wheelchair.

2. Liquid Snake is a genetic clone of Big Boss(Naked Snake from MGS3), and is technically Snake's brother. He is identical in looks to Solid Snake but Solid Snake dyed his hair brown and cut his hair shorter right before the original MGS and that's why they don't look exactly the same. Somewhere in between MGS and MGS2, Ocelot grafts Liquid's hand to his own arm, which you'll recall the Cyborg Ninja from MGS cut off Ocelot's hand, and Liquid's hand somehow takes control of Ocelot's entire body through his nanomachines. A nice rule of thumb is that most of the weirdest shit in MGS is explained through nanomachines kinda like how everything in religious terms is explained away as God is omnipotent.

Raiden was genetically created to be a super soldier. They ran a test run of the original Shadow Moses incident(MGS) in the Big Shell in MGS2 to test his abilities. Don't worry about not getting it becuase MGS2 is a big clusterfuck of a story and really unnecessarily complicated things the same way the second Matrix movie complicated the series far more than it had to.

Naomi Hunter created the Fox Die disease and did a lot of work with nanomachines overall. She is in the original MGS as Codec support and is in MGS4 as some double agent bitch always switching sides for some weird reason. I still don't think they explain why she seemed to be wrapped up on Vamp like a whore (she si cheating vamp to gain his trust, she works for ocelot "the good guy") before you and Raiden take care of him. She ended up dying from her cancer after she injected herself with nanomachine negating superjuice which made her cancer instantly turn on her and kill her, just like cancer always does.

3. I thought the Fox Die was what caused him to age. You might be right though. Or maybe we're both right and it's just another loose end in the story. Hopefully someone else can answer that.

4. Snake's not against anybody in any of the games other than Liquid. Snake is a pawn throughout the three games he's involved in from beginning to end. He is merely a soldier that gets pushed around constantly and overall he's too stupid to question authority even though he's always being lied to.

You're right. I remember that part.

Ok so then why put Fox Die in him then? Isn't that also to keep him from staying around too long? It seems like a redundancy which to me means a story that wasn't well thought out.

I remember it killed Decoy Octopus early on when he was disguised as the DARPA Chief and locked in the same cell as Snake. It killed Liquid at the end of the game. I don't know if it was in Ocelot, probably not since he was a Patriot but who knows, and everyone else was killed by Snake so we don't know about them. Still I thought Naomi said the Fox Die would kill Snake eventually and it was merely a matter of time. However I don't remember her saying anything in MGS4 to back that up or clear it up at all. Wasn't Snake supposed to be dead within a few months of MGS1 ending? I could have sworn she said that in the game, but who knows at this point.

I think that is indeed the case, if not sooner.  However, FoxDie effected different people in different ways, and that's why Decoy Octopus, Liquid, etc. all died at different times.  By MGS4, I believe they had managed to figure out more approxiamtely when different people would die when infected by FoxDie.

1. Nope. Snake's hair was long and blonde just like Liquid's. I hope you have the original MGS on hand so you can see for yourself, or you can attempt to find what I tell you on YouTube. Before you begin the mission in MGS1, you have the option of watching some briefing videos between Campbell and Snake. It's in a dark room and Snake is butt ass naked. Campbell is asking Snake about his retirement and telling him he needs to call him in on this one mission. At the end of the very last video(There are like 8-10 of them) Snake asks for some scissors and hair dye. It's hard to tell during the videos, because of how dark it is, but you can see Snake has longer and lighter hair.

Retraction: It seems in the briefing videos Snake's hair only appeared to be blonde but it was supposed to be brown. Kojima changed it in the Twin Snakes version. He did have to cut his hair however. I don't know where I got the hair dye thing from, but when I Googled about this there were multiple people that also thought he said something about hair dye and got corrected. Here's a pic of the briefing video to show how fucking blonde they made Snake in that video though.

2. I'm not so sure about the second. MGS2 was an absolute mess of a story and overall seemed absolutely pointless to the overall plot. MGS4 did it's best to ignore MGS2 as much as humanly possible to tell it's story. Later on when Campbell seems to turn on you, him and Rose, both of which I guess are programs at this point in time, tell you about being some tool of some group and bred as a soldier or created to be a soldier. Maybe it's just nanomachine control. Everything else in the fucking series gets chalked up to nanomachines so it would make sense that this did also.

Genes don't work like that.  Your basic genetic code should stay the same throughout your life, and it is ultimately cell division that causes things to go wrong after a time (due to cells not dividing correctly, cells mutating, etc.).