So if I had to adjust that (which I would especially now that I know of the demographic problem) I would do it like that:
-3 factions (one secret) no prob at all, they all shall have about 20 members
-Prominent fishing families (200 people)
-Prominent merchant families (100 people)
-Workers (100 people)
-Smugglers (50 people)
-A senior town council member who owns 3 large fishing boats and is looking to expand the industry (he is one of the fishing families)
-A council member whose family has a trade cartel, and fleet of fishing boats, and several trading vessels (all part of the above)
-A wealthy merchant who "garners a great deal of support with the many feasts, entertainments, and other diversions he supports". He is a foppish dandy who enjoys "fine wine, good food, and the latest fashions" as well as a "patron of the arts and spends lavishly to support festivals, plays, and concerts" (yeah he invites the fisher smuggler and trader "high society" so what is the prob
-Smuggling operations sufficiently large that a bungled operation could land "a few respected people in jail" (does not make the city more crowded)
-"Many" fishing boat crews, in fact, enough that it would take "several" going missing before the locals demand action be taken to figure out what happened (200 people most of them being at sea for extended time no one counts them all when they return)
-"the town's various organizations"
-A full time town guard of 100 warriors (That's a bit to many, a standing guard of 25 does the job perfectly)
-A council member whose family has a trade cartel, and fleet of fishing boats, and several trading vessels (n.p.)
-Several popular fishing boat owners (n.p.)
-Can muster a militia of 500 residents (Make that 200 and you are fine, every able man will defend the town no matter if fisher or smuggler)
-A small force of marines (Yeah so add another 30 soldiers if it has to be)
-A jail that can handle punishments including 2d10 years of imprisonment (no one says you cannot throw 20 people into one cell, the only thing unrealistic here is that there were no jail sentences in the middle ages, that would have been much to costly to feed prisoners all the time. You had corporal or monetary punishment, the only ones locked up were awaiting trial or someone come with the extorted money to get free)
-Docks that are "almost constantly busy" with two primary piers for large ships, and a series of smaller ones (like it should with such a large fleet)
-The capacity to build 6 new warships under a commission from the crown (Yeah being boat people they should have some wharf, that's were some of the 100 workers above make there living)