I will explain it to you:
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Yukito did indeed turn into a crow (don't ask me why or how), and was called Sora. As a crow, he relived the experiences he had with Misuzu, except he was kinda looking at himself. As a crow, Yukito did not remember his past experiences as a human until he turned back into a human for a breif moment with Misuzu next to her bed, then turned back into a crow. Nobody knows about this situation.
The flashback to the past was of Yukito's ancestor (the samuri) and Kanna (the girl in the sky with wings), Uruha is just some girl who helped Yukito carry on the task of finding the girl in the sky. So no, Yukito did not go back to the past, that was just explaining how the girl in the sky came to be.
Misuzu died of her dreams because she was cursed (possibly by Kanna, or because she was Kanna's other half, and since Kanna was already cursed, Misuzu shared the same fate). She died happily though.
Those two children in the end i'm not to sure about, however they are poosibly the reincarnation of Kanna and that Samuri dude.