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A lot of it is from raiding, collecting drops, valor, etc. Yes you can do it all through LFR.
As for where you start it.. I honestly can't remember. Wrathion is the main NPC involved with the quests and he's near to the BMAH.
I think you have "Mysterious Note" in your mailbox once you hit 90, sending you to Wrathion at the Tavern
And yes, all raid parts are doable through LFR. Lots of parts have been nerfed, drop rates buffed, and it's generally much easier to complete now than it was at the start.
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