Didn’t realize this got bumped. Played a lot more (obviously), so let me just get to the biggest obstacles to 100% completion:
Legendary ships: By far the hardest part of the game, but if I can take 'em, so can you. First off, get ALL the upgrades (you’ll need to visit the diving bell locations) and make sure your ship is fully repaired.
HMS Prince (southeast) - The easiest. Broadside, swivel, broadside, swivel, rinse and repeat. All you really need to do is keep on the move to avoid its heavy shot; otherwise it has nothing that can really hurt you.
Royal Sovereign and HMS Fearless, a.k.a. The Brothers-In-Arms (northeast) - The trick is NOT to follow the obvious strategy, i.e. sink them one at a time. Why? Because while both are still afloat, neither can use their heavy shot, which is the real danger here. Stay on the move, pepper them both from a distance, and do your best to avoid being sandwiched. You may take a broadside from one of them while you’re focused on the other, but as long as it doesn’t happen too often you should be in pretty good shape.
El Impoluto (southwest) - Its attack plan is simple; build up astounding speed and ram you, then use heavy shot to finish you off. When you see it rushing, sail perpendicular to it at full speed; this is the only way to avoid it. Even if you can’t avoid it completely, with luck it’ll just graze your stern. Then immediately bank hard to get away from its heavy shot barrage. Once the threat is passed, unload on it (only the sides will give you weak points). From there it’s just a pure battle of attrition where you must avoid heavy damage to have any chance. Stay sharp!
La Dama Negra (northwest) - This one’s just cruel. This monster is equipped with a mortar which can fire like 25 shots per salvo, each hit doing sick damage, and it’s very quick on the draw with its heavy shot. Worse, the only part of it that will open up weak points is the stern. I have no fancy strategy here; just stay on the move and get its back if you possibly can!
I’m not entirely sure, but it seems like if you just keep at it (and follow a sound strategy), eventually you’ll prevail. One time the Brothers-In-Arms were no trouble but I struggled horribly against La Dama Negra; another time the Brothers-In-Arms were a pain, El Impoluto was relatively simple, and La Dama Negra was impossible the first three times but went down easily the fourth. There’s no telling.
Mission objectives: The important thing to remember is that you don’t have to get both at the same time. You can clear one, do the other on replay, and it’ll count as both cleared. The ones that might give you trouble:
“Use one broadside to sink two boats” - At this stage of the game, you won’t have much firepower, so just ignore it. When you replay this, your firepower will be what it currently is, making it much easier.
“Kill four gunners” - You’re going to have to run around a bit to find them, during which Prins and Torres are going to get distracted a lot. This actually works to your advantage, as they’ll stay put, lessening the risk that you’ll get too far from them and desync. Take out any meddling guards that get in your way (out of sight); as soon as you see the gunners, drop them with sleep darts.
“Use a fire barrel to sink a ship” - The barrel does not have to strike the ship directly; if you shoot it with a swivel and the explosion sinks a ship, that counts. This is actually easier, so go for the direct hit only if you get a really good opportunity.
“Skin three animals” - While marooned, the only animals you can skin are black panthers; the best way is to hide in foliage, whistle it over, and kill it with the hidden blade. Make sure you get at least two from the first area before proceeding further into the jungle. You’ll get a chance for a third before confronting Vane.
“Double Assassinate Cockram and Burgess” - This can be really, really irritating because this duo apparently has spider senses; as soon they glimpse your fleeting form for a millisecond or hear your breathing, you’re busted. The trick is that they can’t detect you while talking. Climb to the top of the closest house (sleep-darting the tower gunner so he doesn’t blow your cover). Soon after the duo gets within sight, they’ll bark something to a man in a barracks, whereupon you can seal their fate with an air assassination.
“Stay out of combat/use a rope swing to kill the captain” - The rope is in the tower. You have to begin your swing as the captain is walking toward you. If you’ve avoided combat up to this point and miss, be sure to assassinate him immediately so you at least get the first part done.
“Stay out of combat while finding Hornigold” - You only need to avoid detection by other ships before finding The Benjamin (which requires plenty of hard maneuvering but otherwise isn’t too tough). Once on the island, you’re free to go all out against his guards.
“Visit two old friends” - The tricky part (other than the fact that you’re underarmed) is that one of the “friends” is actually 1. an enemy and 2. dead, and you must get to him before entering the prison. His remains are in a gibbet near the shore. Vane, inside the prison, is easy to find.
“Use two guards as a human shield” - You must do this while fighting El Tiburon. Also, if you’re wearing the First Civilization outfit, change to something else before starting the mission, or else it will be almost impossible to use human shields.
Kobal 2 - You can turn off shanties in the options. I’m actually surprised you never tried that.