Dude, love this! I've read the comments so I'm not gonna repeat but echo the major sentiment. Congrats on creating your first adventure, it's addicting! I've been running Pirate Borg for a few years now and vibe with the setting and the Commodore is a fantastic big bad.
Have you ever ran or played INTO THE MAELSTROM? I think this would benefit from more freedom of wandering monsters - that also might open up some space. A random table instead of the pregens (maybe a table for the players to roll on for said Hidden Agendas). I'm running some Pirate Borg this weekend (TLAPD) and might include this if there is time - I will let you know how it goes if I do.