In my first post, I remember mentioning my suspicion about the "original" Muhammad to be some sort of Christian. Even with all the intentional using of words like Islam, Quran, Muslim, Allah etc. still there was a distinctive difference in the way he was expressing things.

Beside the very clear different way of talking about religion and belief, there were also stories that didn't make sense when put together. One said Jews, Christians and Muslims (Islam), the other only Jews and Christians. Because of some problem he was saying something like "There can only remain one deen here". (The deliberate Arabic usage again telling us to think that "deen" is the reference to religion of Islam.)

The confusing thing was that while there were 3 religions mentioned, he was saying "two deens shall not coexist"!

*'May Allah fight the jews and the christians. They took the graves of their Prophets as places of prostration. Two deens shall not co−exist in the land of the Arabs.'*

I already suspected that there were only Jews and Christians and for some reason he wanted the Jews gone but I still couldn't understand how the translator (if they did of course) turned two religion names into three but still translated the rest as it was although clearly contrasting the first phrase.

Thanks to Google, as usual, I accidentally found the answer. I was searching for the Sana codex details and found this awesome site where (a) dedicated scholar(s) shared their extensive research on a lot of aspects of Islam. The interesting thing is that they too have named their study "The Origin of Islam", because probably after noticing some very clear contradictions, they must have realized that the origin was not what the history told us.

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“People of the Book” and Nazarenes in the Koran: Who are the first, and on what grounds are the second included?

From the outset, the problem around the term nasârâ-Nazarene is weighty. Christians never called themselves Nazarenes (except roughly during the ten years that followed Pentecost): what they have been called and have called themselves is Messians (Messianic), i.e. khristianoi-Christians in the Greco-Latin Empire, and its equivalent mešîhâyê in Aramean (and the Persian Empire).

So why would they have been called by a different name in the Koran? Did Christians mistakenly use a different name for six hundred years until Islam was born? Even the most conservative translations by Islam’s standards, the Saudi publishing house dar al-Ifta for instance, do not always translate nasârâ by Christians. Here are two counter-examples:

“Those who believed, those who follow the Jewish [scriptures], Nazarenes or Sabeans, whoever believed in God... will have their reward” (surah 2:62 parall. 5:69). And also:
“Those who have believed, and those who follow the Jewish [traditions] and the Sabeans and the Nazarenes, the Magians and those who associated with God, God will judge between them on the day of Judgment” (Surah 22:17).

This is understandable: throughout the Koran, Christians are accused of giving God associates and are therefore doomed to hell. But the first verse, and the second implicitly, sends the nasârâ to Paradise. Should we think that God, who dictated the Koran, used the same term of nasârâ in these two versesto designate instead the “Nazarene community”? Does God ignore that proper nouns designate unique realities? Is it perhaps a persistent error in interpretation? Or a mistake inherent to the text? But how could it be so?

The key to this question was actually given ten years ago by Antoine Moussali. In a cutting-edge article [1] Moussali pointed to the mechanism responsible for introducing contradictions in the meaning of the word nasârâ in the Koran, particularly in Surah 5. In this surah, we read on one hand:

“O you who have believed! Do not take the Jews and the nasârâ as allies: they are allies of one another” (5:51)
But on the other hand: “You will find the nearest of them in affection to the believers those who say: We are nasârâ” (5:82).

The contradiction is so plain that many versions translate nasârâ by Nazarenes in the second verse. Another problem is that verse 51 is illogical: how can one pretend that Jews and Christians are friends or allies “of one another”? Muslim commentators get over the difficulty by saying that those who do evil are allied to each other. Is that possible if they are enemies, as is often the case? The problem therefore seems to lie in verse 5:51 where the term nasârâ, used just after the term Yahûd (meaning Judaics) can thus only mean Christians. In fact, this passage contains a startling formal inconsistency, as the cantillation reveals a break in the rhythm, which disappear only if we omit “and the nasârâ” (wa n-nasârâ). The balanced text is this:

“O you who have believed! Do not take the Jews as allies: they are allies of one another” (5:51).

Now the verse is clear, meaningful and coherent. Now the contradiction with verse 82 is gone. The convergence of these three factors leaves little room for doubt: the passage was interpolated.

So why was wa n-nasârâ inserted in the first place? Some could even object: was there a serious enough reason for taking the chance of causing a major formal contradiction a few verses further? There is a reason.

Before looking at it, we must make this remark, formulated by Antoine Moussali: Koranic expressions like and/or [the] nasârâ are all interpolations (perceptible to the ear): you find them in surahs:
2:111 (“or nasârâ”);
2:113 (followed by “and the nasârâ say: the Jews have nothing to stand on”);
2:120 (and the nasârâ”);
2:135 (or nasârâ);
2:140 (or nasârâ);
and 5:18 (“and nasârâ”).
In verse 2:135, the addition of “or nasârâ” after “be Jews” is especially devoid of logic: it implies that the “sons of Abraham” recommend that people be either “Jews or Christians”. Without the addition, the verse is again comprehensible:

“They (the sons of Abraham, cf. 2:133) say: Be Jews, you will be guided. Say: Rather [we follow] the religion (millah) of Abraham, as hanîf-s (hanîfan)” (2:135).

This verse acquires rich meaning, and should be compared to 3:67, when also rid of “and not a nasrânî”:
“Abraham was not a Jew but he was a hanîf who submitted [to God] (hanîfan musliman)” (3:67).

The two verses say that Abraham was not a Jew since he was himself the father of the Jews, and that those, relying on their election, did not remain faithful to the religion of their forefather who submitted to God (muslim). The same idea is present in the gospels (for example in Mt 3:9 and Lk 3:8), but here the affirmation is quite ironic as Abraham is presented as model of the hanîf. To grasp the scope of the anti-Jewish polemic pervasive in the Koran but antedating its written form, we need to know that in the Talmud-s, the term hanef means herectic, an equivalent of mîn [2]. By presenting Abraham as a kind of “heretic who submitted to God”, Jacqueline Genot (+ 2004) explained, those two verses turn back against Judaism the Judaic condemnation of those they themselves deem heretic – in particular those whom patristic tradition calls the Nazarenes: if we are heretics, they say, then Abraham was heretic before us: you are the unfaithful heretics!

Why modify the meaning of the word nasârâ?

As far as we are concerned, Koranic expressions of the type “wa n-nasârâ” (unlike other occurrences of the word nasârâ) are additions to the text forcing the reader to think that nasârâ stands for Christians: this isn’t a mere happenstance. But what goal was being pursued by intentionally stretching the word and by doing so truncating its meaning? The historical context furnishes the explanation. If, from the time of ‘Uthmân, the decision was made to showcase the current “Islam” as an autonomous reality willed by God, its Nazarene roots had to be masked, particularly in the writings produced to oppose the Jews and Christians’ Bible – even if, historically speaking, nothing proves that the collected works were officially presented as divine before the 7th century; similarly, nothing indicates that the terms Islam and Muslim had already been employed in the modern sense (before the 8th century, Muslim simply meant one who submits (is subjected) [to God] as we see in the mouth of the Apostles in 5:111 – true to the Aramean root [3] – while islâm meant submission).

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So, after reading this explanation I can only speculate that they did similar changes on the original Muwatta!

You can read the full article here: http://rootsofislamtruehistory.com/subpages/Ahl-al-Kitab_people-of-the-b...
Here's how their research started and took a turn: http://www.lemessieetsonprophete.com/annexes/presentation-en.pdf
This one summarizes the evolution from Judeo Christianity to Islam: http://rootsofislamtruehistory.com/subpages/Genealogy-Islam.PNG
And for much more: http://rootsofislamtruehistory.com/