Coincidentally, I'm about to start a Freeport campaign of my own in the very near future (probably as early as this week!) so this is interesting stuff. I'm not using the modules, though, and I don't remember the details of them very well. I do struggle with standard hooks in modules, which in general I think are a bit weak and rely too much on an assumption of eagerness and general good-will by the PCs (I don't know about you, but my PCs typically don't have a lot of good-will to go around.)
I'd almost have them be hired to do something else entirely; a throwaway mini-adventure, if you will, that somehow gets them embroiled in this whole affair. Maybe Egil isn't quite the mousy, good-natured guy he's made out to be. Maybe he's trying to shake Lucius down and that's why he wants him found. Maybe he's hired the PCs to work as a repo team to get something back from Lucius.
Sounds like you've already got that covered, though.
I agree that as much as I like Freeport, it needs a bit of decamping. The
Pirates' Guide did a fair job of decamping it, but it didn't quite go far enough. I want my Freeport quite a bit darker. The no slavery thing? I'm throwing that out first thing. Slaves will be ubiquitous in my Freeport. I've retooled the generic pantheon to, essentially, be transparent slight respellings of major demon and devil lords. Sometimes they're just used straight; Dagon is my God of the Sea, the Black Prince (Grazazat) is the equivalent of the Pirate God, Moloch is the god of fire/sun, etc.
I tend to go back and forth on which pirate themed city as a mini-setting I prefer; Freeport or Five Fingers. I've decided that the best way to do it, actually, is to just combine the best elements of both of them, and maybe throw in some stuff borrowed from Katapesh, Lankhmar, Sanctuary, Haven, Scuttlecove, and basically every fantasy version of a wretched hive of scum and villainy that I can think of. I might replace the halfling gangs with one of the Five Fingers gangs, for instance. While I like a lot of the Freeport occultism already, I really like the Five Fingers Thamar and Dragonfather cults even more, so I'll probably adopt those.
I'll probably also have a delegation from Mazin in town, tentatively putting out hints of peace talks. My Mazini will be pretty dark, though... borrowing again from the Iron Kingdoms Cryx nation I think. Undead/construct hybrid servitors with necromancer and worse running the show.
As for the serial killer; I think little touches like that go a long way towards making a setting come alive. Do they even need to find out who or what Firebrand is? Only if they really take exception to finding immolated corpses here and there around town. I'd have them find evidence of his passing through, hear some gossip, and leave it as an unresolved and probably unresolveable problem. Unless they focus all their attention on it, of course. Which they can't afford to do because there's too many other, more pressing problems coming at them from all sides.
Anyway, I mentioned this in the other recent Freeport thread, but I created my ENWorld blog specifically to ramble about my Freeport Pbp, so feel free to check it out, comment, offer help or criticism, etc. Maybe it'll be at least a little useful to you, too.
http://www.enworld.org/forum/blogs/hobo/