My rough and ready pseudo-guide would be:
Starting Shipyard settings:
Cannons: Cannonbreaker II; Glass Cannon II; Shipwrecker II; Light Cannon II (5 command points)
Modules: Rum Supply I; Sturdy Deck I; Sharpshooter’s Emblem; Assassin’s Emblem

Getting a couple more good cannons in the first half of your run is always a good idea. The best options are usually swivel guns, light cannons or cannonbreakers, but pretty much everything can be useful. Having cannons that can soak a hit (like heavy cannons) or at least soak a hit in the third round of ship to ship combat (everything that isn’t glass) is a strong benefit. Same goes for modules and crew.

The Sharpshooter’s Emblem and Assassin’s Emblem are the strongest of the class modules, and overall may bias your crew preference towards Musketeers and Backstabbers, which due to the added power of those modules probably end up being the best classes.

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Cutter skill tree:
Cutlass Swing I; Retaliate I; Cutlass Swing II
Shiv’s Presence I; Mermaid Call I
Shiv’s Presence II; Shiv’s Presence III; Shiv’s Presence IV
Mermaid Call II; Mermaid Call III

As with most builds I will advocate for, you want a mix of reasonable HP (to mitigate cannonfire in the ship phase and blight damage in turn based combat), a decent damage staple attack and a secondary attack, ideally a push to push people into spikes or backstabbers.

Class build recommendations:
Backstabber:
(i) Backstabber (3)+Cutthroat(4)+Escapist(3)
(ii) Backstabber (2)+Cutthroat(4)+Assassin(4)
(iii) Backstabber(3)+Assassin(4)+Escapist(3)

Backstab is great, and the escapist tree allows you to make the most of knocking units into them by always being in good places, whilst also providing a useful HP boost to an otherwise fragile class. Cutthroat and Assassin both provide bonus attacks each round and damage boosts, but Cutthroat is the more flexible and easier to use usually.

Spearmaiden:
(i) Spearmaiden(4)+Heavy Arm(4)+Noble(2)
(ii) Spearmaiden(4)+Believer(4)+Heavy Arm(2)
(iii) Spearmaiden(4)+Hunter(4)+Noble(2)

Grappler:
(i) Grappler(3)+Cutthroat(4)/Arsonist(4)+Brawler(3)
(ii) Grappler(4)+Cutthroat(4)/Arsonist(4)+Reaver(2)
(iii) Grappler(3)+Cutthroat(4)+Strongman(3)

Cleaver:
(i) Cleaver(4)+Believer(4)+Reaver(2)
(ii) Cleaver(3)+Sentinel(3)+Tar Smearer(4)

Cleaver has pretty bad combinations of support trees, so I have no third recommendation here, even though other classes have plenty more combinations that work well that I haven’t listed. Even Cleaver(3)+Sentinel(3)+Tar Smearer(4) is more about debuffing armor for your other pirates and is arguably a shade below par. Cleaver(4)+Believer(4)+Reaver(2) is solidly competitive though.

Cook:
Cook is one of two classes with a pretty much mandatory tree – bruiser. Cook(4)+Bruiser(4)+Anything(2) will work ok, but the best option is
(i) Cook(4)+Bruiser(4)+Reaver(2)

Musketeer:
Musketeer is the second class where you really, really need a specific tree to make it work. The Musketeer tree itself provides a borderline useless attack, so you must instead look for Sharpshooter, which allows you to attack every turn instead of every other turn, and hits a solid 5-tile area to boot.
(i) Musketeer(2)+Sharpshooter(4)+Cutthroat(4)
(ii) Musketeer(2)+Sharpshooter(4)+Noble(4)
(iii) Musketeer(2)+Sharpshooter(4)+Trick Shot(4)

Damage boosts are great, extra attacks are great, stuns are great – pick your poison.

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In terms of how I play on Ultimate IX my main priorities are grabbing a cannon or two, making sure to preserve as many crew and modules as I can in ship to ship combat, while eliminating (a) enemy armor (b) enemy HP regeneration (c) enemy HP boosts (d) enemy movement boosts in pretty much that order.

Enemy modules that inflict blight on both crews are a huge asset to you if you can preserve your own rum barrel and destroy your enemy’s. Especially if you have a couple of stuns on your team to keep armor heavy threats out of the fight while they slowly die to their own blight. Always leave these modules in play if you can.

After that just make a point of storing up Abyssal Ether for the final fight. Shrines to the sea goddess offer a reliable +3 and if you get the chance to loot or buy a sacrificial trident or dagger that’s an absolute must pick. Being able to farm ether for more monster uses can easily swing any fight.

When you get to Blackbone as long as you have 5 ether it should be an easy fight. Wipe him off the map on turn 1 with your monster uses (knockbacks into the sea snail egg will do the lion’s share of the work) and then you’ve just got a regular battle to win. Usually you can do this by attrition if he blights his own crew and you preserve your rum supply module. Even if you’re losing the fight you can just add a single mate to the fight each turn and let the blight tick down all the foes – though you almost certainly won’t need to resort to that.