I don't think the word order in the case of estuve en Madrid dos meses/ estuve dos meses en Madrid. Here's why: Substitute the verb pasar (I believe would be a more common usage) for estar and you will note that they are both OK.
Also durante and por seem very interchangeable in the cases you quote, but durante can be used for other things that diverge from por. Example: Durante el mes de junio las noches son breves.
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Me ayuda si corrige mis errores. Gracias.
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