Annelise, This question has remained unanswered because in a way it's unanswerable. Here's why:
It is in the nature of both the Hebrew Language, and of Jewish learning, to force the student to make the connections by him/herself. This was for a number of reasons, including a) to force the student to think, b) to require a teacher and network of contemporaries at all times, c) for brevity, and d) to hint to secondary and tertiary connotations.
You don't need go past the very first Torah verse: "In the beginning, G-d created heaven & earth." Except that's may not be what it says - it may be a reasonable way to "connect the dots", but it’s a way Rashi rejects. Rashi reasons that the word "Bereishis" means "In the beginning OF ...", not just "In the beginning", for which the word BaRishonah would be more appropriate. The translator is choosing the simplest meaning by adding the simplest word: In the beginning OF [the entire process of Creation]. G-d [first] created the Heaven & the Earth. Now the translator must explain why the verse didn't use the simpler BaRishonah or BeTechilah, and why Heaven seems to be created again in verses 6-8. Did we use Bereishis because it connects to other places where the concept of Reishis is found? Because we can assume that we'll begin our book at Creation, so we can reasonably assume your mind will append "...Creation" to "beginning of..."? Perhaps the creation of Heaven in verse 6 is an elaboration of the creation of Heaven in verse 1, or perhaps one is the creation of "Heaven", while the other refers to "sky" using the borrowed term "shamayim" to describe what we actually see when we look heavenward. Rashi (also bothered by how Heaven could be created before a primary ingredient, water, is mentioned) connects the dots by translating it as "In the beginning OF G-d's creation of Heaven & Earth, the Earth began as emptiness & confusion, so G-d said, "There should be Light!"
That’s just the first word. The Rabbis discuss why it was “created” rather than “formed”, why the name Elokim was used rather than Hashem, why the redundant words “et” (which leaves the literal translation as “the the heaven & the the earth”), why the word for Heaven is a pluralized form, why the G-dly name Elokim is pluralized in the first verse of the primary text of monotheism, etc. (Imagine coming to an editor with a book with a confusing first sentence. “You want me to print this book?! I can’t even get past the first sentence! Either re-write it or throw it in the garbage.” Now imagine that book becoming the first book ever printed, and the best-selling book of all time!)
The fact that this would cause disagreements was not considered a big deal. They'll either work it out, or they'll go to a higher authority for clarification, or the next generation will work it out. It's not uncommon for a question to be asked in the Talmud, a series of unsatisfactory answers given and rejected over hundreds of years, then a satisfactory answer given perhaps 300 years after the question was asked - and it is codified into law! We then consider it part of our unbroken tradition.
"But nobody had this tradition for all that time. Isn't that by definition 'broken'?," asks Annelise. The Rabbis look at her uncomprehendingly. "Of course not! It fits the verse perfectly, it fits the pattern of established law, and it answers the question fully. If the glove is fitted, you have acquitted!"
Put into the context of your question, our students have the following difficulties:
A. The Rabbis say on “G-d shall give beauty to Japheth, and he (alternatively, it) shall dwell in the tents of Shem” (Gen. 9:27) that in the tents of Shem, the Torah books will be written with the beautiful script of Japheth (Tal. Megillah 9b), and that this refers to “Ktav Ashurit” (lit., Assyrian script. Secondary connotation: Rich script) which may be used to write Torah scrolls (Meg. 18a).
B. Old Hebrew is very fast and easy to write, Ktav Ashurit slow and painstaking. Both may be used to write Torah scrolls. For fast transcription so that every student has a copy, Hebrew characters fit the bill better. For a beautiful community scroll, Ashurit is preferred.
C. In describing the Luchot, the Tablets of the Law, there is a clear and immediate redundancy. Exodus 32:15 says they were “written on both sides; on the one side & on the other were they written.” That violates our No Redundancy rule of the Torah. The Talmud therefore understands it as “the writing was on both sides, and the writing went through & through”. Rav Chisda then comments that this means that the center fills of the letters Samech & Mem Sofit were suspended miraculously in the Luchot (Shab. 104a). However, in Old Hebrew script, other letters (like Daleth & Ayin) have center fills, but Samech & Mem Sofit don’t. This statement of Rav Chisda would lead us to conclude that the Luchot were written in Ashurit.
D. Ezra clearly established that all Torah scrolls should henceforth be written in Ashurit (Sanhedrin 22). This connotes that previously they were written in other scripts.
The answers mentioned by Annelise are roughly the ones the Talmud proffers in San. 22a. They are theories meant to draw clean lines through most of the sources, and push the remaining sources back into line. After discussion by the Rabbis, we seem to conclude that one fits the sources most accurately & elegantly, and that is now viewed as the accurate tradition.
One helpful way to view this was advanced by Rabbi Samson Raphael Hirsch. He views the Oral tradition as being handed over complete, taught over 40-day-and-40-night marathon sessions to Moshe. The Written Torah then has missing or extra letters, nuances of language, grammar and syntax, etc., to provide a “Map” of the Oral Law in case it needs to be reconstructed. Hence, we have the first judge, Othniel ben Kenaz, using pilpul to re-establish thousands of Halachot (Temurah 16a) and the measures (Yoma 80a), the prophets re-establishing the Final Letters of the Alef Bet (Shabbat 104a), or Ezra, Hillel & Rabbi Chiya restoring “forgotten” Torah (Sukkah 20a).
Additionally, any major “sealing” of the Law was done by international consensus: The Mishna through Rabbi Judah the Prince, the Talmud through Ravina & Rav Ashi, even the Tosafists through Rabbi Shimshon, the Count of Coucy. These men of wealth and influence communicated with communities throughout the world, accepted their input, and after the issues were hashed out put an authoritative “seal” on a body of law that was then accepted by all Jewish communities around the world.