Running Paizo Adventure Paths, with reference to Skull & Shackles

From https://www.enworld.org/threads/your-experiences-with-skull-shackles.667617/#post-7820742

Clarity & Presentation - Paizo write primarily for the reader on their couch, not the GM at their table. The material tends to be incredibly verbose, and often irrelevant to at-table play. I have learned over time how to treat the material as a buffet and not be bound by what's written down. Eg you get a great NPC with a few paras of backstory, who is "Remains in room - fights to death - suicides if captured". The GM can delete that last bit, take her out of her room, create links with PC(s), make her a cool part of their own campaign.

Balance - S&S is known as ridiculously deadly in the early chapters. There is a general issue that 3e/PF balance is very tenuous even to start with, without author 'errors'. I had a lot of trouble running Curse of the Crimson Throne in PF, with the 2 min-maxed PCs slaughtering everything with ease while the 2 non-minmaxed PCs were nearly helpless. I solved this by converting APs over to 5e and making/converting my own stat blocks, with the PF ones as a guide. This is pretty easy, certainly easier than using a multi-column PF BBEG stat block as written.
Re S&S balance in particular, I don't have an issue with most merchant ships being so outmatched they surrender immediately; pirates don't go in for fair fights! I think the main thing there is that pirating per se shouldn't take up a large amount of play time. In Queen of the Black Coast REH covers three years of pirating in a couple lines. The interesting stuff happens when things go wrong.

Minigames - Paizo are legendarily awful at these. My best advice is to ignore whatever mechanics they give you and run the situation the same way you normally would. Eg instead of a chase sequence mini game in Curse of the Crimson Throne, I used a battlemat of rooftops, and the standard rules for jumping, climbing etc. Players will thank you for this, trust me! Likewise, instead of a doing an actual tarot/harrow-card reading & trying to interpret the results, just improvise some suitable NPC dialogue from the reader suitable to the PC - "I see the queen & crown - there are great things in your future, Lord Zerda! But the snake means you must be wary..."

Overall, I find the better PF APs (prob including S&S) to be well worth using, but sadly they are probably least suitable for a new GM, and most suited to a very experienced GM who knows when to ignore instruction. For a newbie GM I'd recommend something like Adventure Anthology #1 at basicfantasy.org