Puzzles, traps, and tricks for a pirate's cache. (PF, maybe some 3.5)

[Togath]

So I've been working on starting a campaign for my usual group of players, which starts with them seeking out a treasure of a legendary pirate said to be hidden on a nearby island... but that can only be reached at the height of a massive(and cursed) storm that only hits once a decade, after sailing past an assortment of dangerous barely submerged rock formations.
So far, the plan is for the lightning and winds of the storm, along with it's strange magic, to unveil a doorway the party can use a key obtained earlier to open, and then delve in to the legendary captain Darce's treasure cache, a dungeon built in to a small island/mountain with technology potentially powered by the storm.
Along the odd things the storm causes are an influx of undead(mostly described as misty ghost-ish and fleshy draugr-type stuff so far) as well as some other creatures. Comozant Wyrds(aka Saint Elmo's Fire but a critter), elementals, chonchons and sea creatures are all some stuff I'd considered.
Level is 3, and at least two pcs can breath underwater, and the party is likely to have at least a potion or two of lesser restoration.
So... anyone have some fun thoughts for interesting encounters I could through at the party? Whether puzzles, traps, or monsters. I feel like wind and lightning powered machinery might be fun, but I'm struggling a little to figure out how to use it(plus using Saint Elmo's Fire or the above mentioned creature based on it seems like it could add a spooky mystical element).

Encounters so far for this arc have been; save a humanoid crab person who lives in the village from setting-specific seabirds that spit a weak poison, encounter what appears to be a shipwreck survivor while n a rowboat, only to find out it's a draugr, and possibly land on the island only to be harassed by chonchons soon after.

Environment wise, the trip there was been wet(both from the wind tossed waves, and from the sheets of rain), and I like the idea of some water having leaked in to the dungeon over the decades. It'll also be nighttime by the time the party reach the dungeon.

Rules-wise, I'm using anything pathfinder by Paizo, Alluria Publishing's bestiaries(Beasts of the Boundless Blue being the main book), and Sphere's of Power(not that that seems super likely to pop up here). I've also homebrewed a handful of things(like the poison gulls) and am willing to figure out the specific mechanics if I can come up with neat concepts. Adapting from 3.5 dnd might open some options too.

[EvulOne]

pits under the water level are always a good thing, combine with eels or something. Old mechanical traps with frayed ropes slinging coral weapons, some water-logged undead, maybe even a few dead-fall traps thanks to trip wires underwater.

[Gildedragon]

Strange storm might produce wild magic effects... Not sure if PF has them but you could crib some from 3.5 or homebrew a few: random energy type shift (positive energy, negative, acid, cold, sonic, acid, electric, force); area changes; target swap; random metamagic suddenly applied to it...

Puzzle: treasure isn't in coin or art objects, but ore; all the walls etc have been rich with adamantine/silver/mithril ore. Hints have been spread throughout the adventure: a room is a massive fire trap, with what looks like a big stone fountain (the foundry); Undead fought during the storm had rusted and damaged weapons of the special material; the final room is an empty half-hewn chamber... Maybe with a couple skeletons (slaves that were made to mine the ore) holding picks and a portable hole full of dirty looking rocks.
Thought: there's two stages to the "treasure" place
The fortification: where we'll armed undead and deadly two-way traps are located; it is, however, easier to get in than get out.
The mine: half flooded, more ghosts and natural perils, from wandering monsters that got in but can't get back out.

[Togath]

Some interesting ideas...
Maybe arcs of electricity shooting through certain areas at intervals too?
And... hmm... maybe some zombie sea monsters?(squid+giant template? Or maybe a zombie giant squid[the non template type] as a boss)Stuff placed there by the oddly savvy-to-magical-phenomena(lore-wise, he likely was something like a duskblade/magus) captain to animate when the storm comes?

As a sort of finale to the arc, I plan to have obtaining the treasure release a huge surge of enchanted energy, that both brands the party with parts of a treasure map on their arms, as well as results in them waking up outside a few hours later not quite sure of how they got there...
Why do I mention that? Because maybe the components that are gathering energy for that kind of thing(which also serves as a beacon to anyone who knows what to look for that the map has been obtained) might themselves also function as hazards. Electrified doors to give a lockpicker a sudden shock?