On my most recent read-through I remembered that, indeed, in Paper Hearts everything in the dreams is extreme-colored. Although it's night, and that probably just explains it.

I think you'll have to imagine that the dreams in Amor Fati looked different to Mulder than they did to you. It would have really confused the audience to see that much of the story that way .. destroyed the illusion of reality that was there for awhile .. and didn't really make a difference, anyway.

What did I miss?

I'm not sure the canon gives a date for his parents' divorce. Sometime after Sam was taken. 12 is close enough, probably.

Yes, Scully's eyes are blue. Ish. Most of the time. Mulder's change color. I don't know if badges say eye color. Driver licenses do, though, and she has one of those that he's probably seen.

I like the last few paragraphs. They're too short to be incoherent.