Why am I discussing internal questions?

Before I answer this I need to define what are internal questions and what are external questions.

External Questions

External questions are questions that come from sources outside Torah. The classic external questions are 

1. The Torah says that the world is 5676 years old but science says the world is billions of years old
2. The Torah says that there was a global flood some 4500 years ago, geology, archeology, etc.  say that there was no global flood
3. ...

Internal Questions

Internal questions are questions that come from within the Torah like the questions that I have been asking. 

There are a number of reasons why I am starting with internal questions:

1. External questions have been dealt with by many, I don't feel that I have that much to contribute
2. Internal questions on the other hand have not been dealt with that extensively because they require a greater knowledge of Gemara, Medrash etc. which many of the skeptics don't have.
3. There is little room for discussion of external questions, believers simply dismiss them, "what do scientists know?" Internal questions on the other hand are much harder to dismiss because they come from within Torah sources.

Conclusion

I know that I probably sound like a broken record but my constant question is where is the mesora? How can it be that basic things like what was given at Har Sinai are not known and are disputed? It was drilled into my head in Yeshiva that Chazal had a mesora for everything even the structure of a Yeshiva (see R' Shach's writings). What internal questions show is that there is no mesora on so many things it calls into question the whole idea of Chazal having a mesora. If they didn't know when matan torah was and they didn't know what the beis hamikdash looked like and they didn't know what ksav the Torah was given in and what ksav was used in the period of the first Beis Hamikdash then what did they know? Why should we assume that anything they say has any basis in tradition? Of course, once mesora falls away then the so does the whole edifice of Torah Shebaal Peh.