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I think the easiest way for Homura to be in the new world as a magical girl is if she woke up in the hospital with her soul gem in hand like before. Maybe that's when she started to remember Madoka. Though that may not be true, because Kyubey probably would have mentioned her dubious origins as evidence of her parallel world theory being true.
I guess I just poked a hole in my own thought, Kyubey isn't weirded out by new Homura, so she probably made a contract with him on normal circumstances, the question is: when? Maybe she was saved from a demon by Mami and met Kyubey then, thinking of him as way to find Madoka. Her wish was almost definately Madoka-related, hence the bow.
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