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The main story only takes place in zones of my alliance?
You can only complete the main quests (those tied to the harbourage) once per character. It's identical for all 3 alliances so there is nothing extra to experience.
You'll be able to explore the other alliances later in the game. The main story mostly takes place in the territory of your alliance, but the general main story is the same for all alliances.
Aye, you'll be able to obtain all the achievements associated with questing, exploring and doing dungeons across all faction zones. The achievements are character bound, as are any titles you unlock for completing them. Dyes you unlock for completing achievements however are account bound.
Beware all ye who log on for here there be typos...