Wake of the Watcher deconstructed

First, let me requote my outline, bolding the parts that have something to do with this module.  You may notice that my plot outline is much simpler, more straightforward, and less... gratuitous fan service of Lovecraftiana, maybe you can say.  But after quoting that, let me summarize briefly the adventure as written and then go through the encounters that it has to see if any of them will be usable in my framework.

• A well-loved professor, Alpon Lechfeld has died in what appears to be an accident—although there are some suspicious clues that cannot rule out foul play.  For the sake of getting the game going, I'm going to tell the PCs that they've all been asked to be pallbearers and are named as (minor) heirs in his will.  He'll give them a few things, but most of his fortune is left to his daughter Revecca.
• Ghosts are appearing in town, threatening (or at least frightening) many residents, that can be traced to a haunted and abandoned ruin of a former prison.  Why are they leaving their normal territory? (linked to the murder above.)
• A rampaging Frankenstein-monster is blamed for some more townsfolk murders.  This, and the ghosts, are probably happening at the same time, so nobody knows which is responsible.
• A mob of townsfolk wants to exhume Lechfeld and "put down his corpse"—of course, it turns out that someone has already exhumed him and dismembered his corpse, as well as apparently eaten some other recently dead in the graveyard.  Notably, an amulet that he was buried with is missing.  Revecca suggests that this amulet kept the ghosts in check in some way; if it's gone, that explains their extraordinary aggressiveness.
• The Frankenstein monster was a creation of Lechfeld himself in an extremely foolhardy experiment years ago, and it has come into town looking for him when he stopped visiting.  It really is a monster, though, not some misunderstood something or other—he's killed numerous townsfolk viciously.
• The ghosts have to be put down (salt and burn their remains) in their haunted house.
• The professor's beautiful and friendly and otherwise hopefully quite sympathetic daughter, is missing.  Gigantic wolf-paw prints and other hints of that nature surround the area she was last seen.
• Her kidnappers are, indeed, werewolves from the Bitterwood, and they've taken her to Innsburough.
• To follow up, the werewolves may have to be confronted in the Bitterwood, though.  They're too good at covering their tracks to be followed to Innsborough.
• The Black Path has Revecca in their grasp, and want to sacrifice her on the Devil's Reef by Otto von Szell, the manorial lord of the Innsborough territory.
• Revecca knows enough about her father's amulet to use it as a key to enter the sealed tomb of Grozavest.  This ability is related to its ability to suppress undead activity in some way.  But Otto von Szell had his own ideas, and wanted to call up some undersea daemon (Typhon?) to destroy his rivals in the Black Path.  Namely, Grigore Stefanescu.
• Stefanescu steals Revecca and her father's amulet, either from the PCs if they've rescued her, or from von Szell if for some reason they don't.  Maybe it's a ghoul group that actually carries out the abduction?  Ghouls from Dragomiresti seems like a good way to bring that into play.
• The ghouls take Revecca to Grozavest, where Stefanescu foolishly intends to "rescue" a Primogenitor sealed in with Melek Taus, thinking that by so doing, he will gain a champion capable of dealing with any of the other noble houses.

The module as written has the PCs chasing a mysterious "Dark Rider" (and never catching him) to Illmarsh, Ustalav's version of Innsborough, only to find a clue there that sends them back to the capital.  Both are, of course, a riff on Lovecraft's Innsmouth, but what the module suggests is that the Deep Ones and in-bred villagers' deal is on the ropes, because mi-go have invaded the Deep Ones home under the water and enslaved them.  Both have brought all kinds of Lovecraftian monsters to bear to try and gain advantage over the other, leading to a somewhat embarrassing collection of fan service where you see just about every Lovecraftian monster that you can think of sitting around in some room somewhere waiting for the PCs to stumble across it.  Anyway, here's the vignettes in order.  Some of them will be useful to deal with the very reduced version of the module that I have, but many of them will be not only superfluous, but embarrassingly so.  Remember, that I may well use names interchangeably; in Timischburg, the ersatz Innsmouth is Innsborough; in Ustalav, it's Illmarsh.  The Whispering Way becomes The Black Path, etc.

THRUSHMOOR This is completely unnecessary in my version of the module, except for one thing that might be desirable.  It's a reasonably largish town that the PCs have to pass through, where they can get all kinds of rumors about Innsborough, foreshadowing how weird and disturbing it's going to be.  If you re-read "The Shadow Over Innsmouth" you'll see that Lovecraft himself uses a similar structure for the same reason; in fact, the protagonist of that story wasn't even going to go to Innsmouth, and hadn't even heard of it before, until he started getting these rumors.

AMBUSH To keep Thrushmoor from being too talky and boring, they suggest that a cultist ambushes the PCs at the livery as they're asking about clues about the "Dark Riders"—a undeath cult assassin with a few ghouls hiding in a hay-wain that's lost a wheel.  When they ask the PCs for help, they wait until they're in an uncomfortable, flat-footed position and burst out of the hay.  Well, as Raymond Chandler said (paraphrased), when in doubt, have some thugs with a gun show up.  Barring guns, some undead thugs sound workable.

SHIPWRECK AND MORE TALKING On the way from Thrushmoor to Illmarsh, the PCs see a ship struggling at some lonely and abandoned quay.  The guy on it is a curious inventor type who's come up with submersibles, but for now the PCs are merely meant to meet him so that they can conveniently go to him and recruit him to help them dive later.  Since I have little interest in exploring the Deep Ones' lair underwater, I see no reason to include this.

THE MAYOR AND MORE TALKING  The Mayor of Illmarsh recruits the PCs (by force, if need be, it says.  Seriously) to help him investigate missing people, but what he really wants to do is take control of the Church, and be even more powerful and influential in town, without a major rival.  I don't have a mayor, I've got an isolated and disquieting manorial country gentleman, Otto von Szell.  Also, since there's no war between Deep Ones and mi-go in my version of this, there probably aren't missing townspeople.  Rather, much as in the Lovecraft original, the PCs are prime suspects to become the next missing people to have passed through town.  And then, in what sounds suspiciously like a joke, the mayor suggests that the Watcher in the Water (sorry, Tolkien, excuse me, Watcher in the Bay) is just a myth, and then as soon as the PCs wander near the docks they get attacked by one, which is a semi-mundane giant octopus, lacking all of the suspense and terror of the attack on the Fellowship by the Watcher in the Water by Tolkien; although a good GM could make something of it, I suppose.

THE CHURCH Churches in Timischburg are Christian churches, but here, it's a church to some sea or nature god or other of the Paizo pantheon.  Of course, in either (as in the Lovecraft prototype) it's not-so secretly a church to Dagon.  Paizo calls it the Recondite Order of the Indomitable Sea, because I guess after everything else, they couldn't just use the Esoteric Order of Dagon.  This is probably one of those scenes that you want to include somehow, but going into the church and starting to just kill cultists as soon as you walk in seems a little... I dunno, way too caricaturishly D&D, maybe.  Presuming that you find the secret doors at the rear of the church, you also end up finding 1) some of the missing townspeople's bodies, with their heads exploded, and 2) "the scion of the sea" a weird lobstery monster (some kind of extra-special modified chuul, to be exact.) And then, 3) the "slug spawn" who look kind of like the ear worms from The Wrath of Khan but who actually cause their victims heads to explode after a few days, kind of like the chestburster from Alien turned up to 11, I guess.  There's this whole thing where the slug spawns protect you from mi-go mental manipulation, but the sad side effect, of course, is that your head will explode.

I actually kind of like the head exploding idea, but I don't think this is the place for me to use it.  I'll save it for something else, probably.  Anyway, after getting this far, the PCs probably suspect the Deep Ones infiltration of town life (especially if they've read "The Shadow Over Innsmouth") but don't know what to make of the slug spawn, and don't know anything about the mi-go thing.

BARON'S HOUSE  I actually have a current, present manorial gentleman who's the de facto authority in town, but in the Paizo version, this baronial authority has been MIA (KIA, I should say) for decades, and his manor is abandoned.  Lacking anything else to do or anywhere else to explore, eventually they're supposed to make their way there where they discover the full details of the Deep Ones nonsense, as well as figuring out that something is seriously wrong with deal between the townsfolk and the Deep Ones, and that there's some greater threat going on under the water still.  There's a ton of encounters here in what is essentially a Lovecraftian dungeon, but few of them, in my opinion, have adequate explanation for why they would exist other than as a guided tour of Arkham Country, with Lovecraftian monsters as attractions in an amusement park.  I could potentially use... some of these, I guess, but nowhere near most of them, because they make little to no sense.  Anyway, here's a (more or less) complete list of stuff you find here.

• Poor victims of the Deep Ones breeding program, who are now also victims of something else (see below)
• A swampy giant of some kind (not sure why? Bodyguard of the vizier, or something?)
• lots of cultists
• the cult leader, who's head explodes and he turns into a pseudo-Dark Young of Shug-Niggurath on being defeated in combat (not kidding)
• spectres, who are the ghosts of some old tax collectors killed by the insular townsfolk years ago.
• yellow mold (ok, that's not necessarily Lovecraftian)
• hounds of Tindalos, who are lurking around waiting to ambush the PCs in some room for some reason.
• a shantak (yeah, flying around near the balcony hoping someone will walk out so he can attack them.  Sometimes I hate D&D, at least as it's poorly played and conceived.)
• a moldy plant thing—a variant shambling mound is what they use for stats, but it somehow manages to feel very Lovecraftian in a pseudo-original way, actually.
• plenty of Deep Ones (they call them scum in Pathfinder, based on the D&D monster of the same name.  It's kind of absurd that there are several riffs of the Deep Ones in D&D—sahuagin, scum, locathah, kuo-toa, etc.  Anyway, scum is what we get here.  FANTASY HACK goes straight to the source and just has Deep Ones.  They're public domain, anyway.
• A colour out of space, complete with a well of sorts for it to hang out in.

SUBMARINE DESCENT I don't envision that my PCs will ever take a submersible down to the Deep Ones lair (or even ever conceive of something like a submersible, for that matter)  Besides, Deep Ones don't live in "lairs", they live in cities like many-columned Y'ha-nthlei.  In any case, this is chock-full of superfluous encounters as well, most of which I wouldn't even use even if I were to do anything with this segment, which I won't.

• a "devilfish" attack (a kind of mini-kraken)
• plenty of Deep Ones (ok, these aren't superfluous, at least)
• dimensional shamblers
• some kind of weird "fungus oracle"—it's just a big fungus mouth with tentacles and short stubby legs.  I guess the Paizo folks decided that a Zuggtmoy vibe was really Lovecraftian—which certainly isn't untrue, but I'm not sure specifically why they're supposed to be associated with the Deep Ones or the mi-go either one, except for "the fungi from Yuggoth" which I don't think is meant to be taken too literally.
• mi-go, by the way.  You'll fight a few.
• a gug (yeah, I dunno.  The flimsy excuse is that the mi-go are doing all kinds of weird experiments in here)
• loads of brain cylinders
• and finally, it ends with a fight against a Dark Young.  Then, while they're on their way back to the surface, the mi-go laboratory that covers the Deep Ones lair collapses.
• as an aside, they propose that the Deep Ones will eventually return and things will return to normal before too long.  Assuming that the PCs don't massacre everyone in town for being a vile cultist, of course.