Hm.
While nothing like what you're looking for, I developed an "under-tree" dungeon, of sorts, once.
It was very simple, but it was meant to be - this was a different system.
Mine turned out to be a large spiral, with the outer "segment" of the spiral leading to twelve different entrance/exits, and the beings that inhabited said dungeon having the ability to (kind of sort of*) move earth and stone shape the passages every once in a while - otherwise, each entrance had a similar effect that opened/closed itself based on time of day. This allowed the caves to seem short and uninteresting to nosy would-be explorers, but allowed the creature(s) inhabiting the place to go in and out when they pleased. Each entrance led to a tree who had some roots extend down the very deep tunnels into the sacred spiral.
The wall of the spiral was thick, but had many holes, sort of like Swiss cheese - this allowed defenders to utilize them as either methods of sending physical swarms through, or using certain ones akin to arrow slits (with a heavy rock that could be "closed" on the slit to "seal" the space from the inner part of the wall).
The spiral was (supposedly) a sacred place went through seven different pools of water - each getting deeper, cleaner, and more pure than the last (there was a mandate against clothing; the PCs, of course, ignored this). Each pool had an increasingly deep and long wall that either went above the surface, touched the surface, or below the surface, and each pool was supposed to represent one of the seven deadly sins (the idea being that by washing yourself clean, you came to understand the purity of the essence of a given sin, while simultaneously literally physically purifying yourself). Though nothing like this existed in-setting, having something like the waters of Lamashtu (or whatever it's called) could be really thematic.
The deeper you went in, if female** and undergoing the rite, the better your darkvision became; for everyone else, the darker the layer became, instead, even swallowing other light sources and eventually shutting off all darkvision but its own (kind of like deeper darkness).
At the center were three thrones - the thrones of the coven. It isn't really possible to translate these into PF rules, exactly, but each represented one of the central sins to the coven - pride, lust, and sloth. Carved from crashed meteor (basically adamantine or starmetal^) and mingled with crystal (kefheru^-deep crystal^-crysmal^), the stone spiral and thrones presented a potent source of power - however, to truly make use of their greatest power, you must not only sit in the chair, but remain for seven consecutive 24 hours.
()
The only creatures here were a low-grade 5th level commoner (though she had some arcane powers*), a captured priest and captured psychic wildcat (they were in a deep pit that functioned as a shadow well of power to those who were on the thrones - to most others it is simply a pit, not that they could see it in the darkness.
I don't know how much of this you can use, but there's what I had.
*
**
^
EDIT: Ninja'd by an official module being linked!
Do you need help with coming up with puzzles and riddles?
Oh! One thing I didn't mention, though I really should have, is that the whole thing was as powerful as it was because of that ancient meteor (the metal and crystal stuff) and had been carefully crafted by a trio of hags several centuries prior to civilization moving in. They kind of got possessed by their own stuff, though, and the throne of sloth died of starvation while staying on the throne as she refused to give up the power, even when she was in desperate need of sustenance. The latter two eventually worked a sustenance effect into the thrones (though it took seven days to function), and sat there until they died of old age. The balance was broken, however, and neither wished to disadvantage herself relative to the other (see below), so their servants went uncalled and left alone until eventually they were forgotten about.
That pit that the priest and psychic cat were in was more than just a pit: it was the well that blood sacrifices were poured into (always the blood was originally supposed to come from the throne-keepers or "unrighteous" intruders who had refused to properly purify themselves - or any male that wandered in) and also was able to be used as another method of entrance/egress: those on the throne could use it to scry on and to open one or two gates between any existing pool of water "in the area" - not well defined PF game terms, but the local lands had a bunch of small pools and a few lakes - not to mention the seven pools for ritual cleansing - that existed. From there, they could use any of their abilities through that, or even summon a powerful water elemental. Each use of the a thing and portal and summoning abilities hurt them, though - it doesn't translate to PF, exactly, but each use required 3/5ths of their health (the system used a health track instead of ho) which could be split among all participants... after one of them died, however, the other two descended into paranoia that her sister might try to kill her when she was weak, if she took more damage, and so the powers went unused.
The entire area was infected as a shadow well - that doesn't mean much in PF terms, but it was kind of just evil: like unhallowed and desecrated, except that undead weren't welcome there either - plus tapping into it could corrupt you, and the lingering malevolence could manipulate you into doing evil. Maybe stuff like haunts or the new corruption rules? I'm not familiar with the latter and the former only kind of fits, but not well.
Each throne represented a boost to magic power - again, it doesn't translate, exactly, but it's kind of like a +12 boost to caster levels based on the throne's association: sloth (Conjuration), lust (enchantment), or pride (illusion). Note the translation isn't 1:1, but it's pretty close. Envy (both divination, in this case, instead of abjuration) ran through the thug as well.
Hope all that helps!
EDIT: the campaign setting and game system is Blue Rose, if you're curious. Health is two tracks of 5 boxes - one for lethal and one for nonlethal -, while all "arcana" (magical effects and abilities) are skill-based, with a will save against fatigue for each use thereof. Hope that helps!