tl;dr: Plunder & Peril, because it sounds like more fun. (I also detail a lot of my plans below for the beginning of the AP)
While reading books 1 and 2 of Skull and Shackles the mood caught my attention but I don't think my players would like the pace of them / how unconnected they all feel from each other. The seemingly random encounters in book 2 felt too... I don't know... "have the players randomly sailing around being pirates through encounters that read as if they'll get boring fast and put in these set-pieces" but then the more focused story starts in book 3.
Don't get me wrong, I love the idea of the first two books but I find myself wanting more fun and adventure.
So instead!
I'm planning on running book 1 of Serpent's Skull but place it on an island in the north-eastern area of the Shackles, add in most/all of Bonewrack Isle, and replace the last dungeon with the dungeon at the end of book 1 of Skull and Shackles, have a ship rescue them at the end which brings them to the starting town for Plunder and Peril, while working in parts of book 1 and 2 of Skull and Shackles.
Some of the NPCs from the first two books of Skull and Shackles will be used from the beginning of the campaign. (Notably Sandara Quinn and Isabella Locke). Isabella has part of the puzzle that Lanteri needs, so she'll likely be the one missing at the beginning of the campaign. (I may decide to have it more hidden on her, but I haven't figured that part out yet.)
I'll likely place Plugg, Scourge, and some pirates at the end of book 1 of Serpent's Skull in order to tie in Harrigan a little and I'm currently mulling over how to have him connected to what Captain Varossa Lanteri is after. Maybe he's the not-actually-dead husband (someone bringing him back to life makes sense), or maybe he's just aware of it and wants it. If I'm clever enough I'll have a way to point to something even greater on the Island of Empty Eyes at the end of Plunder and Peril, as a way to encourage the players to really want to join the regatta rather than simply have it be "because it's in the book and you should want the glory of winning it"
With how much of a sandbox Skull and Shackles is, I'm really hoping to pepper in a lot, if not all, of the encounters written for books 1 and 2 because I really do like them, I just don't like the pacing. Bonewrack Isle will definitely be used, Rickety’s Squibs would be a good idea to go at the end of Plunder and Peril, the events in book two will be fun to spread out through Plunder and Peril as well as into book 3, the Dominator will be used if it ever feels appropriate, Ghost Ship? OMG! YES! I hope I can use Tidewater Rock and Mancatcher Cove.
To tie in Harrigan, Plugg, and Scourge I might have the latter two on board pre-campaign. Their plans go a little awry and they're captured by grindylows along with a couple of their own allies and Isabella.
OH! Or Plugg and Scourge are in charge of the Man's Promise and the campaign starts with the Man's Promise attacking the ship the PCs are on, mutual destruction, and the crews have to work together to survive (a la Star Trek: Voyager). Plugg and Scourge can try to gain allies among the NPCs while the PCs can do the same... the information Isabella has is the end-goal for both sides. When the Magpie Princess approaches the final battle between sides takes place! (They can name-drop Harrigan / the PCs can possibly over-hear the two of them talking about him so that they learn why Isabella is important.)
To tie in Harrigan, Plugg, and Scourge I might have the latter two on board pre-campaign. Their plans go a little awry and they're captured by grindylows along with a couple of their own allies and Isabella.
OH! Or Plugg and Scourge are in charge of the Man's Promise and the campaign starts with the Man's Promise attacking the ship the PCs are on, mutual destruction, and the crews have to work together to survive (a la Star Trek: Voyager). Plugg and Scourge can try to gain allies among the NPCs while the PCs can do the same... the information Isabella has is the end-goal for both sides. When the Magpie Princess approaches the final battle between sides takes place! (They can name-drop Harrigan / the PCs can possibly over-hear the two of them talking about him so that they learn why Isabella is important.)
At that point couldn't you just have the Wormwood and Harrigan attack as well? Or instead and as the ship the PCs are on get's too badly damaged Harrigan could just bail and leave Plugg and Scourge behind. That might make the start too long I guess.
Or perhaps they get too close to the Shiv so Harrigan steers away having heard the stories
I'm not sure Plugg and Scourge are necessary NPCs and I'm not sure the island works with them competing - but perhaps just make it be kind of a soft competing to prompt them not be insular within the party.
As I mentioned elsewhere I didn't really try and make a smooth transition between the books. I had originally planned to make one PC the grandchild of Jemma Redclaw and the daughter of the former captain o the Wormwood (who was killed by Harrigan). That is kind of what is implied. I deliberately wanted to avoid the "Harrigan is your father" thing but my players actually seem like they want that. And I originally did not realise that the PC actually could pass for Harrigan's child until my group started playing with Heroforge more than a year in. So I need to try and re-work that given I used a potion of shared memories to have a flashback with Redclaw, Redclaw's daughter and Flint
I'm really bad in that I don't think I wrote it down so I don't remember exactly how much I revealed or implied! I'm actually going to need to ask my players. Doh