I have made Act 1 use this structure so far for my Nightmare levels:

Duncraig Cellar (TPs, player spawn, stash, safe zone) -> Undead Caverns (WP) -> Duncraig (NPCs, WP) -> Duncraig Sewers (WP, Den of Evil replacement)

This renders two issues.
All of the listed are preset levels, yes. But the Duncraig and Duncraig Sewers levels have a problem.
I can't go to the Duncraig Waypoint. All other waypoints work fine, including Duncraig Sewers. Duncraig uses the WP #50, could this be an issue?
Duncraig Sewers has an issue. I turned it into a Preset level and now the quest won't complete. It will say "Eliminate the forces in Duncraig Sewers" but it won't actually get to "5 monsters left".
Can someone help me?

the game has a max of 112 waypoints per difficulty, so the ID isn't the problem. the den quest is only bound to the level ID(8), could see anything that would screw it up if it became a preset, unless the Quest Record assigner got buggered or the pRegion stats are missing(which I doubt as nothing would spawn properly)

duncraig? like the uberquest in median

Contrary to popular belief laz didn't invent duncraig, its from the D2 lore(the novels), as is alot of things he uses(just take a look at the D3 and D2 sanctuary maps)

ok

It just seems to not work, period. I can go to the waypoint in town and waypoint to other locations but I can't go to the location, so it is quite possibly a levels.txt or d2mod thing.

I've gotten rid of all the flying monsters in the sewers (a Bat Demon and a Wraith clone with different names, disabled the flying flag in monstats.txt, but I have no idea why the quest isn't working)

And to kidpaddle94, my Nightmare mode is going to be roughly based on the events of D3, and my stuff is actually going to be almost parallel (as much is it can be with what we know of locations and monsters) with the storyline stuff.

The location near Duncraig is fairly swampy (or would be) and you will have to travel through the sewers to reach outside wilderness levels because the gates are sealed off.

The story is that 20 years after Diablo roamed the earth, comets fell to the sky near New Tristram and demons roamed the earth again. The hero has aged 20 years, and as such he/she has been branded a criminal because they just arrive at the city of Duncraig at the same time demons dig into the sewer system from the outside and burn down a section of the town. The Hero breaks loose from his binds and slays the real traitor of Duncraig.

Here is the levels now:
Duncraig Cellar (portal, stash, safe zone) -> Undead Caverns (wp) -> Duncraig (wp, NPCs) -> Duncraig Sewers (wp, Proving Grounds quest) -> Blood Woods (wp) -> Southern Retreat (wp) -> Traitor's Domain/Berrengher Homestead (traitor quest/wp)
The rest I haven't made up yet.

I remember having the same problem but cant remember if/how i solved it.
Something to try would be extract CaveWSpec.ds1 - resize it and use it as base for the new preset map

One thing to check is that you have an entry tile for the wp(when i added a wp to the blackened version of tristram we needed that), also can you activate the wps? And use them to travel to town and such?

I can activate the WP and travel away but not to the WP. All my other WPs can be traveled to and from and activated just fine. (Except for the one I place at the Den of Evil entry, which is odd, I can get near the actual entrance (I can see the entrance but not the WP) and it crashes my game with DungeonTestGame, the same when getting near the exit in DoE)
An Entry tile? I don't think I've ever seen those before, whenever I add one the other preset levels its a simple matter of making a 2x2 square and adding the type 2 object

I'll give your suggestion a try Volf.