Although title starts with the term historical. We won't be depending on history. This will be mostly based on understading and interpretations of Quran itself.
It is straighforwards clear that Arabs were heavily dependent on Jews about learning how to read Quran. Understanding and extracting rules was important part of establishing religious authority especially after killing each other. Arabs probably didn't have much choice. This is not much of a matter a debate because of many reasons. Putting similarity between Hebrew and Arabic aside because it is considered very natural. Similarity between in some traditions in Judaism and Islam is obviously very suspicious. Especially because many of practices not mentioned in Quran at all but somehow pretty much same in both religion. I will try to show extent of traces left by Jewish teachers.
But historically people have their opinions about understanding the texts. Especially in the periods of Seljuks it seems like they were suspicious of current Arabic understanding and there was a war of understanding until Ottoman era when nobody really give much thought about it anymore.
Today it may seem like there are many occurances that doesn't sounds like nice about Jews. But this wasn't necessarily the case throughout the history. Those understandings are based on more volatile outer layer where interpretation can change quickly. If you examine terms related to definition of Jewish terms pattern is clear. Terms relates to jews are always based on positive roots.
The term for Jews in Quran derives from root related to guidance and originally probably teached to be something like guided ones. This is pretty straightforward. The term for jews straightforward means something like guided ones.
If you discard dots added later. The word where means sons in this construct means prophet in other contexts. Even the word interpreted as Israel is very similar to another word for prophet. Words always have many meanings. Understanding Quran is not much different than playing a lottery unless you believe someone other than Allah.
It seems like during this era alternative understandings and pronounciations suggested. But this part will be too speculative for now. But it is clear there was a war of understanding during centrues around 1000. And because there was never solid understanding especially for certain parts and letters and Quran was believed to predict future. They probably didn't hesitate to suddenly discover verses that blames others with changing recitation. Probably after Seljuks some verses started to be understood as mentioning a false deity called “Taghut”. Directly blaming people with following this deity or evil path. Somtimes context is rebellion and questioning, sometimes directly used in context of blaming some people with not believing and transgressing. Possibly referring to Seljuks. Because they didn't blatantly believe. Disbelievers blamed because they are allied with “Taghut”. Although it is not possible to know what exactly happen this is just speculation.
New writing styles appeared around 900-1000. One referred as "New Style" in corpus coranicum seems like didn't really lasted long. Modern style is very similar to styles appeared around 1000.
Non of those marks are necessary part of the text. Some dots in old mushaf may make it seems like those dorts are part of the text but there are only there to distinguish potential conflicts and some cases possibly to mark integrity checks. Amounts of marks are countless and probably all of those marks reflected on understanding of text after 1200-1500. Over the time text is bombarded with marks until there is not left any space for adding more marks.
Today because of dots same words can have opposite meanings.
This is very limited and probably doesn't really matter much. Although coming to today I don't think letters are distinguished correctly. Letters can change their shapes absurdly but this is mostly about how letters interpreted rather than how their shape changes. If we were to directly consider changes in shapes probably most prominent one is Kaph (ك) letter. I didn't check manuscripts throughly for when did it first appeared but it probably changed intentionally around Seljuks to distinguish it better.
Textual integrity of Quranic text is pretty much clear. Variations within old manuscripts are limited to certain changes except errors which happens only in few manuscripts. Other than differences between Aleph letters and word splits involving this letter there seems to be only other variant is about how Lam letter written because of inability to distinguish this letter based on pronouncation. This actually indicates that Quran was never pronounced correctly nor well understood historically rather it was understood based on symbolic patterns. Probably because pronounced same. Lam Eliph letter is written as combination of La + Vav letters instead of Lam letter itself. And in some mushafs repeatedly so it is wasn't like mistake because they think it sounded same they also think probably it wouldn't matter. And this letter today assumed to be combination of Lam and eliph letters which is actually not the case. It is a distinct letter. This confusion probably arises from the name of “Lam eliph”. It seems like they were calling each letter eliph but later they started refering only eliph letter as eliph. (Also it seems like sometimes Lam Eliph + Meem instead of A + Meem, This one is probably Rare. One instance is 2:75 (كلا م ا لله) CorpusCoranicum mushaf ids: 613, 1553, More than 8 other old mushaf it is without LamEliph. Modern online mushafs other than ones refered ash Uthmani uses Lam Eliph. Less frequent variant occurs also at two other verse (9:6, 48:15) in two other occurances common variant is what used in all modern mushafs. So probably it is written without Lam Eliph. This error should be related to pronounciation.)
It is clear that aim was to preserve textual integrity. Probably they were referring letters by their names rather than direct pronouncation of words when copying. There is ZERO reflection of word groupings in modern understanding, on early mushafs. If words was groupped like modern approach, people would add more spaces after words at least sometimes without intentionally. Put aside this even verse distinctions are not standard. Does not exist in most of early mushafs. This one is complicated topic. There is one other type of grouping which seems like more common. And there is another marks sometimes put withing but exact purpose of those marks is not clear and they are not common at all.
All evidence suggests current understanding of Quran is not very accurate if almost not usable at all.
Eliph and Vaw laters are probably related to seperation of words. Not implying that they don't have any effect on pronouncation. But because of how Vaw letter understand currently there are “And”s everywhere. Sometimes groupped with Aleph and means “or”.
Academics doesn't give much thought about logical consistency of texts because they don't have much expectations. But anyone who consider it may be words of the One, should have higher expectations.
Assuming this text was meant to be easly understandable to people who live in Arabian Peninsula and by Bedouins who barely know any language. It is probably understood through shapes and different type of connections between them. I am not claiming it wasn't meant to be pronounced but there is reason for connections between letters because they represent uniform concepts. Uniform throughout the text. For instance it is pretty convenient to distinguish the word for "Allah" (not claiming it actually pronounced as such.) because it is not just a combination of letter but it is a distinct single unit in the text.
Every unique shape (uniterrupted chain of letters) has to have uniform meaning throughout the text. Currently it is not this is not the case also same words isolated by adding diaritric marks and dots. There may be words with 30+ meanings.
At least as a disclaimer I should say I think Quran meant to be pronounced in Turkish. Or at least a language that sounds very similar to Turkish. But I am not sure if this apply to all of the Quran. Maybe until a point sometimes there excerpts that means “with Turkish pronouncation” but after probably surah 52. It is straightforward readable in Turkish.
There is nothing consistent about current understanding of Quran. Meanings attibuted may have some truth probably because at one point people were able to understand it to some extent. But can only read for inspirational purposes only.
According to Islamic literature it is considered that Quran gathered after prophet's death. Although this is matter of debate and obviously we would have integrity issues if this was a case. But what everybody considers true is that hadiths (explanations of prophet) wasn't even allowed to be written. Hadith literature gathered centuries later. So the debates about Quran's not written during prophets live are probably relates to Arabic translations or explanations of Quran. And because nowadays people are not aware language of Quran is actually not in the langauge they assumed they also confuse historical literature. This is partially because at that time they didn't even had perception of distinct language. Language simply consisted of simple conjunctions and words from many languages. For instance because of stories about Rome fire, words that sounds like nero associated with fire (probably relatively big in size.). But Umayyad introduced this concept and made Arabic language a taboo. Although Arabic just relates to connected writing style. And this language mostly teached to them by Jews. So this is overall how. Still Arabic speakers are mostly unable to understand Quran. Especially in its original form they would understand nothing. So trying to explain Quran is not in Arabic is craziness. I can give countless examples because just as I said nothing in consistent in the current way of understanding Quran. (Turkish words that still used for things that connects from one point to another. "Ara": distance between two point as noun or also to search as verb. “Araba”: Car; “Arap at": Arabic horse). The case for Hebrew is not much different. And actually ironically probably Quran is in Arabic (letters that form single distinct meaning written connectedly) because they mixed up words. It seems like this is mentioned in Quran and said thus we made easy. (According to current understanding at least.) (In torah words splitted wrongly mostly based on spaces introduced later to text. The Alaph letter that assumed to be only vowel letter in Hebrew actually a marker for boundaries. Although some other letters ends words without needing it.)