This got me thinking about what I would do to unify the harbor quests; below is my take on it.
New players would be directed to Kobold Assault; however, its ending would be substantially different. A powerful kobold shaman instead of the usual troglodyte comes out at the end of the quest, and instead of the characters being able to defeat him the shaman casts a powerful spell that sends the characters back to Stormreach. Just as the characters are about to be teleported away, they hear the shaman say something along the lines of "Our new master will bring great power to the kobolds!" This sets the stage nicely for the overlying theme of Stormreach being overrun by kobolds.
Players would then do the quests in the harbor that are infested in kobolds, but for slightly different reasons. The Coin Lords would send the characters to take out two prominent kobold chieftains, in other words Durk's Got a Secret. After this, the Coin Lords would instruct the characters to assassinate a powerful kobold shaman and take over its stronghold, the stronghold being the Butcher's Path. However, the Coin Lords would then discover that the kobolds have enlisted the aid of a powerful troglodyte, and off the characters go into Garrison's Missing Pack.
After completing these four quests, the Coin Lords would piece together the cryptic comments that the various creatures in each of the dungeons made and realize that the mysterious "new master" was staying at the Bonebite Hideout. Convenient that the quest is already called The Kobold's New Ringleader, is it not?
Unfortunately, the characters are not strong enough to take on such an imposing creature and the forces of the Coin Lords are otherwise occupied, so they must enlist the help of Free Agents to aid them. The Free Agents naturally demand that the characters help them first, so they do Smuggler's Warehouse and the Baudry chain in return for their aid. Not comfortable with making Stealthy Repossession a requirement.
Finally the characters enter the lair of the New Ringleader and, with the aid of the Free Agents, kill the new ringleader... a beefy ogre.
Anyway, I think that this would do a good job of unifying the harbor quests, but some tweaks would have to be made to the quests.