I'm just tired to make theories,I'll wait patiently for Gosho to reveal everything.I'm not saying you're right or wrong...But I do admire you for putting so much effort to explain how subaru could be two persons in deguises.
Concerning amuro's flashback it was clear it was Elena,she looks exactly like the woman we saw in volume 42,and since Amuro said he met Ai's family...Gosho didn't exactly reveal anything about her,he just said he will explain later why Elena appears in Amuro's flashback.
As for the mystery girl,I personally think it's the middle brother.Conan guessed it's a girl but he could be wrong (just like he was with Sera).Also the girl seems to be very smart,and looks a bit sick.It could fit with what Sera said,since for her Akai is the strong brother ,and the middle bro is the smart one.
Finally her hair color is different from Sera and Akai,that also fit with what Sera said,about the middle bro who doesn't ressembles Akai and Sera.But I think Chekhov already listed all the possibilities concerning that little girl.^^
Just a side note,I think you should read Gosho's interviews,because he sometimes give important clues concerning the plot(for example he revealed that Amuro/akai rivalry isn't about Akemi...)