And Mary the daughter of 'Imran, who guarded her chastity; and We breathed into (her body) of Our spirit; and she testified to the truth of the words of her Lord and of His Revelations, and was one of the devout (servants).66:12
At length she brought the (babe) to her people, carrying him (in her arms). They said: "O Mary! truly an amazing thing hast thou brought!
O sister of Aaron! Thy father was not a man of evil, nor thy mother a woman unchaste!" 19:27-28
As a preamble, you presumably accept that Mohammad was consulting with both Jewish and Christian holy men when he was receiving the Revelation, indeed such things are actually referred to in the Qur'an. This of course does not disprove the Qur'an as a sacred text, but it is something we need to bear in mind when considering the arguments that follow.
66:12 and 19:27-28 lead me to suppose that Mohammad confused Miriam (the daugher of Amram (Imram in Arabic) and sister of Aaron and Moses with Mary, the mother of Jesus, because this seems to me the most likely interpretation. I'll try to explain why.
Firstly lets look at the biblical references to Miriam:
Now the name of Amram’s wife was Jochebed, daughter of Levi, who was born to Levi in Egypt. And to Amram she bore Aaron, Moses, and Miriam their sister. (Numbers 26:59 NET Bible)
Miriam the prophetess, the sister of Aaron, took a hand-drum in her hand, and all the women went out after her with hand-drums and with dances. (Exodus 15:20 NET Bible)
There are also various reports in the non-canonical gospels which could have led Mohammad to conflate the two (apart from the obvious Mary/Miriam confusion in Arabic). Both women are reported as frequenting the temple and dancing before the Lord, for example.
So we have Mary who is called Miriam in Arabic. We have the Miriam in the old Testament with a father called Imram and a brother called Aaron. And we have Mary in the Qur'an with a father called Imram and a brother called Aaron. Now I'll try to summarise your argument:...
You maintain that Mary's father was actually Imram (The evidence in the Qur'an is the only evidence we have for this, since Christians believe it was either Heli or Joachim) and that she perhaps had a brother called Aaron or perhaps that's how people were traditionally referred to.
I think we can dispense with former explanation of Mary actually having a brother called Aaron (and if some Islamic scholars have suggested this, they need to go back to their studies) because Mohammad has already explained it all to us:
Sahi Mulim 5326: Mughira b. Shuba reported: When I came to Najran, they (the Christians of Najran) asked me: You read 'O sister of Harun ["Aaron"]' (i.e. Hadrat Maryam) in the Qur'an, whereas Moses was born much before Jesus. When I came back to Allah's Messenger (may peace be upon him) I asked him about that, whereupon he said: The (people of the old age) used to give names (to their persons) after the names of Apostles and pious persons who had gone before them."
So the Christians of Najran were suspicious as soon as Mohammad told them about Mary/Miriam having a brother called Aaron. They suspected straight away that Mohammad had confused Miriam with Mary. Mohammad's followers even had to ask him to clarify, since they were unaware of the "linguistic device to denote family line".
We thus KNOW that Mary did not have a brother called Aaron (otherwise this is the explanantion Mohammad would surely have given) and we are thus left with the second and only other explanation - that of "the people of the old age giving names to their people after the names of the apostles and pious persons who had gone before them."
Really? Why choose Aaron out of all the pious people who have gone before? And it's not as though Aaron was a recent pious person, after all. He seems to have been chosen from approximately 1,400 years before. WHY? And why call Mary "SISTER" of Aaron and not "DAUGHTER" as might be expected in the circumstances? And why Aaron and not Moses if were choosing a prophet/pious person to sound impressive?
So my question I suppose is this: If you believe Allah makes things clear for us in the Qur'an, then why should he have chosen to quote a reference to Mary as the sister of Aaron - knowing, as he would (being omniscient and all that), that this would inevitably lead to accusations of confusion with Miriam because of the problems highlighted above?
None of this will convince believers, I realise - I recount my reasoning purely so that you may perhaps understand when I say that so much in the Qur'an (for those who have no reason to believe in the first place) is suggestive of human fallability.
For those who want to believe then of course there will always be possible alternative explanations.
(And, of course, let's not forget that because I'm doing my research and finding these niggling problems which prevent me from believing, according to your religion I will have to burn in Hell for eternity as a result of my unwillingness to "BELIEVE BECAUSE IT'S THE WORD OF GOD"...)