Henry said:The gods wouldn't be that big of an issue, as the gods don't take an active hand, it's mostly through their worshippers - be they serpent people, or priests, assassins, etc. The Cthonic elements are also easy to assimilate: The Daelkyr and the Cults of the Dragon Below would fit easily there, but I swear not being able to run Madness in Freeport unadulterated would be a crying shame.
I don't think I agree. While the Unspeakable One might be easy to treat like one of the Eberron cults, Harrimast and Yarash are a different story. In Black Sails Over Freeport they both take very active rolls both in the adventure and in the history of Freeport. However (trying to solve my own problem) in Eberron you don't have to be a god to have clerics and worshipers. Perhaps the correct question to ask is, "If Harrimast and Yarash aren't gods, what are they?"
Morrow