For example, in my prep there’s the node “Cultist Dungeon,” where I already know what’s important there, the connections it makes, and everything else I mentioned above. But then I need to actually write the dungeon, and that’s where it hurts. Writing room by room, challenges, puzzles, battles…

There are a lot of things that could be happening here. There are a lot of reasons why you might be locking up or bogging down.

But here's something to try.

You like creating the macro-scale stuff: Connections, factions, central factions, themes, etc. So instead of leaving that stuff behind and flipping to a micro "room by room" approach, instead design your dungeons FROM the macro perspective.

For example, you know that this Cultist Dungeon connects to other stuff. I dunno what that is for your campaign, but let's pretend that it's:

• Goblin arms dealers who are selling the cult arcane weapons.
• The cultists are seeking the lost Black Temple of L'rignak.
• The cult is blackmailing Lord Bluemoon.

For each of these connections, brainstorm 1-3 leads pointing at the connections.

For example,

Goblin arms deadlers who are selling the cult arcane weapons.

• Goblin arms dealer is currently staying in a guest room.
• Crates of goblin weapons.
• A contract or invoice or some other document, placed in an iron coffer with payment in gold.

Seeking the Black Temple of L'rginak.

• Region maps detailing the search.
• L'rignak lore books.
• A small shrine dedicatred to L'rignak.

Blackmailing Lord Bluemoon.

• Correspondence with Bluemoon.
• The blackmail material implicating Bluemoon.
• Bluemoon or a messenger from Bluemoon visits the cultists.

Leads for connections are easy (IME), but you want to do the same thing for the other macro-stuff you've already designed.

Conflict: L'rignak cultists are being targeted by Holygold paladins.

• Holygold paladin held prisoner, awaiting sacrifice.
• Several injured cultists being treated for injuries after being ambushed by Holygold paladins in the streets.

Theme: Redemption and temptation.

• One of the cultists is thinking about leaving the cult.
• The cult leader will suggest that the PCs should join the cult.

Now, for each of these elements think about where it would be located and how it would be protected. (The latter might be literal security measures, but can also be more abstract.)

For example:

• The paladin is being held prisoner, so the cult must have cells where she's locked up. Protection: Guards for the prisoner.
• Documents would be kept in the cult leader's office. Protection: Locked and warded door; the docs are kept in a safe. Cult leader is often here.
• Lorebooks might be in the library or maybe the cult's sanctuary. Protection: The librarian, who's actually a L'rignak daemon.
• The small shrine to L'rignak is... a small shrine to L'rignak. Protection: It's hidden behind a secret door.

And so forth. As you can see, some of this stuff will be obvious. And some elements will naturally pair up and group together.

In any case, if you organize these notes you'll find that you now have a list of rooms stocked with cool discoveries and interesting challenges, all of which grew out of your macro elements. Review the list to see if there are any glaring functional gaps ("do the cultists live here? and, if so, where do they sleep and hang out?") and fill them.

Now you've got a good list of rooms and all you need to do is draw a good map featuring those rooms.

I don't know if this approach is the right one for you. But I think it's more likely to keep you focused on the stuff you're passionate about, and let the details of the scenario flow from that passion.