How can there be machlokes if Moshe got the whole Torah from Sinai?

This is one of the most basic and obvious questions that are asked. If as Rashi says at the beginning of Parshas behar מה ענין שמיטה אצל הר סיני to teach us that every mitzva was given at Sinai with all of its details, then why is the Gemara full of Machlokes?

This question can be asked on 2 levels, the theoretical and the practical.

On the theoretical level there is in fact a fundamental dispute about this very point. There seem to be a number of distinct opinions about why there is Machlokes (see Halbertal for a full discussion):

1. Geonim, Rashi and others - Retrieval view -  Moshe received the entire written and oral Law, and at its source, tradition was complete and perfect. The entire halachah was revealed and transmitted to us through a continuous unbroken chain of scholars who received from one another. Through time, forgetfulness and carelessness (due also to harsh political circumstances) this knowledge eroded. Machlokes arises because of the students, who did not clarify the complete details of all the rules from their teachers, and therefore are to blame for the crisis in the transmission of tradition and for the rise of controversy
2. Rambam - Accumulative - Moshe received a subset of Torah Shebaal Peh at Har Sinai plus the principles (13 middos) necessary to derive additional halachos.  Alongside the received tradition from Moshe, Chazal introduced new interpretations of the Torah of their own invention based on the middos. The halakhic process in the Rambams' eyes, is therefore accumulative, each generation adding substantive norms derived by their own reasoning to the given, revealed body of knowledge. The sages, equipped with rules of derivation, deduce from the given material of revelation - both oral and written- new norms which in turn become part of the accumulative material of halakhic knowledge. Only in relation to the newly derived halakhos controversy emerges, since these hermeneutical inferences are not strictly logical inferences where a deduction necessarily follows from given premises. In the received normative material transmitted by the sages of each generation controversy according to Rambam never occurs. In his view, the phenomenon of controversy is therefore restricted to the normative material which is newly derived by hermeneutical inferences. In fact the Rambam strongly criticises the Geonims position:
"But the opinion of one who thought that also the laws wherein there is disagreement are received from Moses, and that disagreement took place due to an error in receiving the tradition or due to frightfulness, i. e., that one [disputant] is correct in his tradition and the second errs in his tradition, or he forgot or he did not hear from his teacher all that he should have; and he [who holds this opinion] offers as evidence for this what they said, "When the disciples [of Shammai and Hillel who had insufficiently studied, increased in number, disputes multiplied in Israel and the Torah became as two Torot" . Behold this, as God knows, is a despicable and very strange position, and it is an incorrect matter and not compatible to principles. And he {who holds this position] suspects people from whom we received the Torah and this is falsehood.".
3. The Ramban, Ran, Ritva are somewhere in the middle. They explained as follows: When Moshe ascended to heaven to receive that Torha they have shown him forty nine reasons for prohibition and forty nine reasons for permission concerning each rule. He asked God about this and God answered that the matter will be given to the sages of Israel in each generation and the ruling will be as they decide.

These are 3 fundamentally different approaches to machlokes but even more importantly to what was given on Har Sinai. If we think about this each shita has a completely different view of what was given to Moshe.

According to the Geonim Moshe got all of the knowledge, period. However, according to the Rambam Moshe only received a subset. According to the Ran Moshe got all the information but not all of the decisions. How can there be a dispute about this fundamental point? How can we not know what was given to Moshe at Har Sinai?

On a practical level we can ask (these are just examples)

1. Bnei Yisrael received the mitzva of tefillin at Har Sinai and presumably started to make hundreds of thousands of pairs of tefillin to wear and Moshe Rabenu presumably instructed them exactly how to make the tefillin including the order of the parshiyos. After that initial period, everyone who became Bar Mitzva needed a pair of tefillin and you would think that they would simply copy/pattern an existing pair. So how could there ever evolve a different order of parshiyos, unless there was a period of time when people stopped wearing tefillin and the mesora was lost. What other answer can you suggest?
2.  The Rambam himself writes in Hilchos Shofar (Perek 3) based on the Gemara (RH 34a)
that Bnei Yisrael forgot what sound a terua is because of all the trials and tribulations of Galus and therefore R' Avahu was mesaken to blow all 3 (shevarim, terua, and shevarim-terua).This is very difficult, my 5 year old son knows the difference between a shevarim and a terua and can make the different sounds and it is a public mitzva done in front of everyone. How can it be that everyone forgot the sound unless there was a long period when the mitzva was not observed.
3. it is very obvious that the Tannaim and Amoraim were missing major pieces of information regarding the set up of the Beis Hamikdash, the daily avoda, and the Yom Kippur Avoda. There are disputes galore in the Gemara Yoma about historical facts, some examples that pop into my head, there is a machlokes Tannaim  was there 1 curtain separating the kodesh hakodashim from the Heichal or 2. There is a 3 way machlokes about the path that the Kohen Gadol took to go to the Kodesh Hakodishim, there are various disputes about the order of the Avoda and how the Kohen Gadol did the Avodas Haketores on Yom Kippur. We see clearly that the Tannaim and Amoraim had no mesora on these issues and were trying to recreate the facts based on sevara and pesukim.

If this is the case regarding the Avoda why would it no apply to other parts of Torah as well. Take for example the medrashim about the Avos. Why should we think that Chazal had a better mesora about the Avos then they did about the beis Hamikdash? Of course the same could be said about other halachos as well. The bottom line is that we see from the Gemara itself how fragile the mesora was and how much was lost so why should we believe in any mesora at all?

In fact, the Navi in a number of places states that Bnei Yisrael completely forgot the Torah. Rhe Ramban al Hatorah says this (במדבר ט"ו:כ"ב) when talking about how the entire Jewish people could sin בשוגג. He writes:

In our sinfulness, this has already happened in the days of the evil kings of Israel, such as Jeroboam, that most of the nation completely forgot Torah and the commandments, and the instance in the book of Ezra about the people of the Second Temple. 

The Ramban writes that in the times of the first Beis Hamikdash as well as the time of Ezra most of the Jewish people completely forgot the Torah. In other words, most of the people had no mesora whatsoever. If so, why should we believe what the chcachamim say in the Mishna/Gemara is the mesora?