The answer to that's going in the hopper

The answer to that is a dupe.

I don't see the clip from the return as having already been here

I ind of love James' Song to be honest. It's probably the low point of the series, but t's so low (and so drawn out) that it's also one of the most Lynchian moments, too. It's just so ridiculously bad that it almost has to be deliberate, and yet they play it so straight.

I'm almost sure that it went through, but I can't find it. So, in my opinion, if you can't find it, it ain't a dupe.

"Deliberate low and drawn out" was the entirety of The Return.

Short answer is that no one really knows. Many fans are assuming as canon that evil Cooper somehow impregnated Audrey soon after the end of Season 2 and before he left Twin Peaks never to be seen for years. However, this doesn't seem to be supported by anything in the show, so I don't know why so many people latched on to it. The timeline in Secret History of Twin Peaks is that Audrey was in a coma for a little while after the end of Season 2 and didn't come out of it until evil cooper had already disappeared. *shrug* I dunno.
The father being Billy Zane seems more consistent, but whatevs. There's definitely something hidden and weird there. Audrey clearly is not in "reality" as we know it and, interestingly, no one on the show mentions her.

As for the whole New Mexico sequence, your guess is as good as anyone's. How it ties into the series is pretty ambiguous at best. Obviously it has something to do with the birth of the Woodsmen, the creation of BOB, and somehow ties into "The Experiment" (the weird creature that appears in the glass box in the first episode) but who knows. It's pretty out there. Sarah Palmer didn't grow up in NM, so I doubt the little girl is supposed to be her. I think it was Lynch playing with an abstract concept like the creation of the atom bomb essentially increased evil in the world or something.

It's possible more pieces of the puzzle will become clear when the next TP book comes out later this month.

I always assumed she was in a coma all along and snapped out of it.

Her performance is so very good kn this though

Wait, that was already mentioned. So there's that.

I just assumed that was a sarcastic asshole thing, like racist white dudes calling black people "boy" and shit like that. "Son, we gotta problem." Doesn't mean the person is literally your son. Apart from that, I don't get where people are assuming this from.

Im confused about the timing, from the last episode of season 2 it would seem as audrey exploding and evil cooper arriving is within days. So he essentially raped what I assume is a burn ward patient.

Which I guess would be in his character, but raping an intensive care patient that I assume is under constant monitoring would take some serious chops, which again would be in his character, so it does check out.

As for his motivation he did it because he foresaw having an offspring decoy would be useful. Or he did it just to destroy the purity of good coopers relationship to audrey, or both I guess, which also checks out.

Well, it hasn't really been explained, though it's possible the Final Dossier might actually go into more detail. In "Secret History" it is mentioned that Ben Horne virtually never left Audrey's side while she was in the hospital.

For now, the actual timeline of events is: Audrey goes to the hospital in a coma, Evil Cooper goes to the hospital...Doc Hayward sees Cooper in the ICU leaving Audrey's room, Evil Cooper disappears from TP (after presumably murdering Garland Briggs and destroying Listening Post Alpha), Audrey at some point regains consciousness, has Richard, tells Richard about Cooper, Richard follows Evil Cooper when he sees him kill Ray, Richard tells Evil Cooper his mom is Audrey, Cooper kills Richard. There's not much to go on, really.