I've been watching these forums for a while now, but having a bunch of obscure questions to answer gave me the motivation to finally join and show off how much of a nerd I am. So, thank you! Anyway, let's see how many of these I can answer and haven't already been answered:

Why/How does the universe end if Snowman dies?

Doc Scratch gave her those powers, somehow, as part of his preparations for English's entry. (2311, 2555)

How the hell does John know what trolls look like? (pg. 1714)

Terezi included an image of herself in the map of LOWAS she sent. (1685)

Why are there two sets of ruins on Alternia? The whole red and blue team thing was never real!

Yes, but it's a special "bifurcated session" that's meant to look like two separate sessions. Why this is is unclear, but it could be representative of the fact that the kid and troll sessions, too, appeared independent, but were, in fact, intertwined.

What’s the deal with the doomsday device? (pg. 2131)

Thanks to Scratch and the Handmaid, apocalypses are a big cultural thing on Alternia. In the books' author commentary, Hussie implies that since a dragon egg is involved in the device, Redglare may have put it there.

Why did Snowman tell Terezi to exile Jack Noir? (pg. 2532)

As revenge for Jack exiling her. (2555)

Why did Dream John blink out of existence instead of just falling asleep when Vriska woke him? (pg. 2647)

Dunno, but he also disappears when he wakes up on page 2951, and they're both similar to Vriska's disappearance on page 3129 when she's transported to her dream quest bed on the Battlefield. Maybe if you fall asleep in midair, Skaia transports you somewhere safe?

How did Rose know how to contact Doc Scratch?

Maybe the horrorterrors told her? Sollux was able to figure out how to contact him, after all, (2256) so there is a way.

Why do the ruins seen on pg. 2283 look so similar to the ones Darkleer was hiding in on pg. 3755?

I mean, it is his descendant's land. There's probably some deeper reason, though, idk.

DS says he told Rose to not look into the orb (pg. 3786), but both pg. 3632 and pg. 3638 contradict this. Was that not him?

I guess this counts as a """warning""": "Would it be so difficult to believe a young lady could be unwittingly apprenticed by more powerful entities who meant her potential to be realized later through some arbitrary trigger? ... What would you say if I said a reserved girl enamored by what dwelt in shadow was selected by the horrorterrors for service, and did their bidding at every step while convinced of her own autonomy?" (3632) And Scratch is all about the technicalities.

How did Jade know about the yellow yard? (pg. 3871)

It's mentioned in Prospitian prophecies. "Though we adore Him we shall never enjoy His beauteous Croak. We spill our blood on acres of black and white so they may cross the yellow yard. At last in Skaia's reflection through broken glass He may find the pond in which He's meant to squat." (3695)

How does John know that? (pg. 3952)

Typheus told him, probably. (3953)

Why does that frog look like a rainbow drinker? (pg. 3980)

I think it's just glowy, since it's a big part of the god frog and all. What seems relevant to me is its eyes glowing in the beta kids' colors. (This is, imo, one of the biggest loose ends in Homestuck.)

Doc Scratch left the blue arrows out for Hussie, so he knew he was coming. Why didn't he do anything? 

The arrows are for the reader, though, I think. Even if he did know, though, he already accomplished all of his goals.

Why is Doc Scratch a lifeless puppet when Hussie's around? (pg. 4077)

This is tough to concisely answer, but TLDR, Scratch is sort of an alternate author figure. And there can't be two authors in one place, I guess???? Hussie goes way more in depth about this in the book commentary.

How the fuck did Gamzee get the Warhammer of Zillyhoo? He doesn't even use hammers, he uses clubs!!! (pgs. 3679+4085)

By being a zilly clown, obviously. And he also has a jokerkind specibus. (3452)

Why does Hussie need the characters to go through the yellow yard?

Not quite sure what you mean by this?

Anyway, I think that's enough for one post. I'll cover some of the Act 6 questions later.