All of the numbers have lead up to the Secret Thread where there is a secret word that finalizes the game.
If I'm not mistaken, there are only these two threads. There are some "CMR" threads too but Gantic said they weren't needed and we have all the clues. The first puzzle's solution doesn't seem to have any bearing on this one, so I think we can safely exclude it.
It looks like we're supposed to connect all the dots or something, but the only significant posts here by Gantic are teasers or saying people are wrong, and the only hint in the Secret Thread is to come back to this one for clues "that will lead you to the end." It's a one-word answer, but he also said "The answer is like right there!" which implies the word is not in code and has been actually typed.
I can only find one unexplained quote...
One. Who said I didn't know? I only said I didn't think it would be coming out so soon.
2. This still isn't solved yet.
D. There is not number three.
I would assume the word ties up all the "loose ends" and relates to the puzzles as a whole, since he said "journey." I hope it isn't something silly like "uzzle" or "clue."