Come again? Why doesn't it work?
Alduin was floating around because of the Dragon Break. He may have reappeared earlier, but then was he dragonbroke again? Does Paarthurnaax not know about it? What did Shor do that made him float around longer then an Elder Scroll? The scroll only delayed Ald for a few hundred years. Shor told that [censored] to wait a few thousand. Rather than expanding on stuff like Alduin, Shor, and Wulfharth, Bethesda simply added new info with no regard for previous lore.
More importantly, The Songs treat Alduin as the Dragon God of Time, who fought Shor in creation.
Skyrim treats him as a good dragon who went bad during the Merethic. Akatosh and Shor are (indirectly) treated as allies, but then is Shor all for the kalpa cycles or something? Akatosh apparently tells Alduin to eat the world when the time comes.
Edit: Man, I really can't spell today.
Edit 2: The Songs still make sense as a whole, it's just the whole Alduin thing that seems rather fuzzy.