The only thing about Thunderspire that isn't Eberronish is the temple to Baphomet. Which could be switched to one of the Dark Six (The Mockery works), or perhaps some cult dedicated to one of the Lords of Dusk.
The Placement of Thunderspire is pretty easy. According to the KotS conversion notes, Winterhaven is on the Southwestern edge of the Icetop mountains in Northern Karrnath, and 200 miles from the Ironroot mountains. So, you can set Thunderspire in the Icetops, or teh Ironroots. Alternatively, you could drop it into the Mror Holds, which is next to Karrnath.
The only thing LACKING is any level of double-cross, less straight-forward story, etc.