Where can I find well documented source material by strictly orthodox Rabbis or scholars which directly address most (or all) of the major themes of academic biblical criticism such as, but not limited to:
As mentioned by @WAF, R' David Zvi Hoffman wrote a response to bible criticism in the early 1900's which is available on Daat.co.il.
Umberto Cassuto, while not strictly orthodox, published a book in reply to the DH in 1941. There are some notes on it here, and a new edition is available online here: http://www.shalempress.co.il/download/Products/29_3_2011_55_29_cas%20gen.pdf
R. Nathan Lopes Cardozo has also written on the topic, and an article of his is available on Aishdas.
Others have taken accepted many of the DH's claims, but made them fit with Orthodoxy. R. Mordechai Breuer wrote how God gave the whole torah to Moshe, but it was a Divine combination of texts. An english discussion of his views appeared in "Modern Scholarship in the Study of Torah: Contributions and Limitations", and Hirhurim links to some relevant articles.
Some have taken an approach that many would find issue with (it goes against the Rambam et. al.), that stress that the Torah is divine, but may not have been 100% given to Moshe. Marc Shapiro recently started writing about this on the Seforim blog.
With regards to the last issue, one does not need to believe that every letter is from the original Torah. This is discussed in "Fundamentals and Faith" by R. Y. Weinberg from Ner Yisrael. It is clear from a number of places in the Talmud that there may have been minor textual errors over time, such as the discussion of Ezra comparing the text in three different Torahs. The Talmud itself also cites pesukim slightly different from our Torah. Traditional belief is just that the overall Torah is from Moshe, but not necessarily that there was never a letter omitted by a scribe. This means lower criticism, while problematic, isn't in the same category as higher criticism.
Jewish society and practice are based on a single, well-known account of their founding. It states that in the year 2448 on the Jewish calendar, an entire nation gathered at the foot of a mountain in the Sinai Desert and witnessed G-d speak. They made multiple copies of the written record and had them spread among the people. They passed on their eyewitness accounts together with the copies of the record to their descendants, teaching them to read the record publicly and observe the many rituals it contains. This is called the Torah.
The suggestion that at a later date someone introduced a change into that account represents the biggest conspiracy theory ever proposed, because it would require an entire nation of people to all knowingly agree to (and live by) the same lie.
It is true that people make up stories and confuse details, but only when one or two people tell a story to those who were not there to contradict them. It is much harder to fool someone if you are telling them about themselves.
We are talking about the common history of a nation. People would notice if their own family history suddenly changed, and would certainly object if that change made demands of them as the Torah does. Getting an entire nation to go along with such a scheme is simply implausible. Additionally, the challenge of coordinating a nation to tell the exact same lie without the use of modern technology would be insurmountable. This is assuming it was done intentionally, because to happen accidentally would be all the more difficult.
This notion is explored by the earliest Jewish thinkers, such as Saadia Gaon, Maimonides, and the Kuzari. See Tzvi Freeman, Lawrence Kelemen, and Jonathan Sacks for modern treatments.
Two other sources one may want to check:
