Maybe Corpus Coranica will help answer some of those questions.
I myself think the Quranic text was finalised BEFORE the islamic history was totally wrtitten (1) . I also think you have different layers of text within this book as additions were made along the way to include stories that people thought necessary to have in that book (2). There were some alterations to the text but there were few I think though their impact might have been important.
1/ I think only the rasm.
2/ I do not think so. The stories (Q 12, Q 18, etc) are in the rasm and were not added. Here or not, moreover, these stories bring nothing to the theology of the text.
(1) This is the only solution I can find to explain why, when you read the Quran without the islamic exegisis, verses that islam tell you are related to Muhammad are in fact biblical writings. For me, the Quran nevcer spoke about Muhammad, Mecca, and the rest. Tafseer writers just corrupted the meaning of the text.
1/ Nope, there's other solutions. I never read the Quran with Islamic exegesis, since this one knows nothing about the text.
(2) The fact that the text mixes midrash writings and christians apocrypha writings is for me the proof of such textual layering. Those texts come from different period and therefore, except if you believe in the Quran as God revelation to mankind, they could only have been collected together but at different dates. There are many other clues to this layering (the Lord vs Allah in many suras is another example).
1/ Nope it proves nothing.
2/ Then any writer which draw today (2018) from 15th c. writing or 18th c. prove that his writing comes from the 15th c. or the 18th ? How's that?
3/ Use of different word proves nothing I'm afraid.
(3) The reason why we know some of the texts went through alterations comes from the islamic tradition itself that tell us about this guy who meets another guy and hear him reciting a surah and is puzzled because he never heard this sura recited that way. He then takes him to see Muhammad and explain his issue. Then Muhammad ask both men to recite that sura and tell both of them that they are right in their reciting. This is what later islamic tradition will call ahruf in an attempt to hide the fact that the text that had been circulating was not 100% the same depending on the copies you could put your hands on and also to explain away the slight alterations that were being made.
1/ the problem you describe is the "readings"problem it only proves that there was no oral tradition to read the rasm, as many people read it therefore recite it differently.
It was the same rasm, but perforce, as the narrative affirms the unity of the hearing of the "prophet" proclaiming, the narrative affirms an oral tradition. But the reality is exactly inverse hence the fact of what you describe: "the islamic tradition itself that tell us about this guy who meets another guy and hear him reciting a surah and is puzzled because he never heard this sura recited that way. " It's perfectly normal, as the oral tradition is a myth, there was therefore different "reading" as never those who had the text were together in Mecca/Medina/Zem Zem and hearing the "prophet".
2/ It is the same rasm.
Topic: Qur'anic studies today