"Dead Man's Quest" is an adventure by Graeme Davis that appeared in Dungeon 107 (February 2004), and is designed for four 1st-level characters.
Throughout: Skithis's racial bonus feat is marked as such, but the humans' bonus feats are not.
pp. 90-91, Gun Deck; Gunpowder Storage: According to Freeport: The City of Adventure (Supply and Demand, p. 148), Kolter has not yet experimented with something the size of a cannon, because the volume of powder needed would be highly vulnerable to fire spells. The multiple cannon and barrels of powder on Fletcher's ship are therefore highly unusual for the setting--either Kolter has progressed to larger weapons, or Fletcher found another source for firearms. Either explanation would have a profound impact on Freeport, and could serve as hooks for future adventures. DMs who wish to avoid introducing this concentration of firepower into their games should replace the cannon with ballistae (as suggested in the adventure) or with the smaller swivel-guns described in Freeport: The City of Adventure (pp. 150-151).
Update: By the time of The Pirate's Guide to Freeport (five years after the events of the Freeport Trilogy), some mainland dwarves have started to produce cannon (Education, Technology, and Magic, p. 26).
pp. 93-94, H3. Shrine to Sekolah: Srathulas: Add "rebuke undead (2/day)" to SA. Give her two domains and their granted powers. Death and Water seem most appropriate, giving her "death touch (1/day)" and "turn fire creatures or rebuke water creatures (2/day)", and making either cause fear or obscuring mist her domain spell (mark it as such with a superscript "D").
pp. 94-95, H5. Mother Merrow's Quarters: Mother Merrow: Insert "/19-20" after dagger damage. Ride should be +11 (5 ranks, 2 Dex, 2 feat, 2 synergy). Give her a spell component pouch.
Skithis: Familiars are magical beasts, not animals; add "darkvision 60 ft." to SQ. Familiars use their master's Base Atk and base SV, unless their own is better. Skithis should have Base Atk +3, Grp -8, Atk +7; Fort +2 (own), Ref +5, Will +6. Hide should be +15 (5 ranks, 2 Dex, 8 size); Listen and Spot should be +8 (5 ranks, 1 Wis, 2 feat).
pp. 97-98, The Temple of the God of Pirates: Black Sails Over Freeport gives a name to the God of Pirates (Harrimast), information on his temple (pp. 30-34; see also Freeport: The City of Adventure, p. 96), and a stat block for Peg-Leg Peligro (p. 215). (Update: The Pirate's Guide to Freeport (pp. 145-146) and 3rd Era Freeport Companion summarize and update much of this information.)
pp. 99-100, U1. Front Doors: Cult Priest: Insert "+3" after "HD 3d6" for his Toughness feat. Insert "/19-20" after dagger damage. Hide and Move Silently should be +3 (0 ranks, 1 Dex, 2 feat). He should have one more feat at 6 ranks; Knowledge (religion) +6 is an obvious choice. Give him a spell component pouch and wooden holy symbol (Yellow Sign).
pp. 100-101, U7. Unspeakable Temple: Mordekai: Insert "/19-20" after dagger damage. Spellcraft should be +11 (7 ranks, 2 Int, 2 synergy). This still leaves him with 4 unspent skill points, so raise Knowledge (local) to +9 (7 ranks, 2 Int). Add Disguise +3 (+5 acting) and Gather Information +5 to his skills; neither is trained, but both have synergy bonuses from other skills (Bluff and Knowledge [local], respectively). Of Mordekai's four conjuration spells, one is a ranged touch attack and two are summon monster, leaving only one with a saving throw. This means that Spell Focus (conjuration) by itself is a poor feat choice for him; either replace it with another feat or replace Persuasive with Augment Summoning (which has Spell Focus [conjuration] as a prerequisite). Give him a spell component pouch.