1 - On Rambam and Kabbalah - I saw in V. 3 of Igrot Kodesh of the Lubavitcher Rebbe (letter to R' Y Leiner - earlier note in same letter discounting Redak and Abravanel (on Yirmiyahu) on Keri and Ksiv is alos of interest) that he has a tradition in his family going back to the Besht that the Rambam was "a great Mekubal". He questions this based on the statement in Shar HaGilgulim that the Rambam was משמאלא דדיקנא דזעיר אנפין ,etc.
2 - On Precedent and Autonomy - In a letter to R' Zevin the Rebbe cites ShuT Divrei Nechemiah that the Alter Rebbe admitted that he placed to much weight in the opinion of the Achronim (especially the Magen Avrohom) and that he later decided to follow his own opinions to a greater extent (usually for Kabbalistic reasons - this is why his Siddur which was written later is considered more authoritave)
3 - I am surprised that so little attention has been given to the discussion of the conflict of Torah and Science in the thought of the Rebbe (this is what Rambi has I , II). I believe that it was in order to investigate this that the Rebbe went to Berlin.
In the first letter in Igros Kodesh V. 1 to the Rogatchover  he points out that all the Rambam's science is taken from the Aristotle  . I erred in my previous post when I wrote that he believed the Rambam's science infallible. It seems his desire to defend the Alter Rebbe was so very great that he was even willing to violate his own anti-apologetic stance .
The Rebbe's use of medievel scientific concepts is in general in need of clarification. For instance, he has a really brilliant explanation of the Mishna in Pesachim 2,1 based on the Greek idea of four elements and the fifth element of the "hylic matter". The explanation is eminently plausible and quite possibly an excellent example of "Hellenism in Jewish Palestine" but I can't quite see the Rebbe taking a "positive-historical stance".
There is an entire book on the subject of Emunah U' Maddah in the Otzar HaChochmah (and one in English as well.)
I'd also like to point out that in all of the letters that I looked over I didn't catch a single Messianic reference (except for one negative statement about Messianism). Contrary to Deutsch, I believe the Messianism must be a relatively late development in his thought. 
 Interestingly, the Rebbe realized right away that the letter of the Rogatchover in Dovev Sifsei Yeshonim was a forgery see his sharply worded letter (there are two) to Bloch in Igrot Kodesh (V. 19 or thereabouts)
 R' Deutch, Larger then Life printed several fascimiles of the Rogatchover's letters I don't remember if he has the reply to this one.
 In a different letter he writes that the Hirschian model of "raising difficult questions and providing insufficient answers" is no good either for Israel or the US. It is true that apologetic was very important to German Orthodoxy (see Prof. Breuer's book on the subject) but I don't know why he identifies R' Hirsch as the founder of this approach.
 It is almost impossible to engage extensively in Kabbalah without involving some level of Messianism - cf. R' Avrohom Abulafia, Ramchal, R' Kook, the Rebbe. etc.