Similarly, R' Zevin in many places makes light of the Roshei Yeshivot who out of fear of "originality" like to "blame" their chiddushim on the Rambam. And the Seridei Eish has many times differentiated between the methodology of the historical Rambam  and the Rambam of the yeshivos.
It is the purpose of the first essay of the book to demonstrate that the historical Rambam did, in fact, make mistakes, phrase statements inaccurately, etc. and that a critical student needs to keep these options in mind when studying Rambam. I believe that Prof. Shapiro has proved his thesis admirably.
Here are several notes relating to various topics mentioned in the book:
1- Pg. XI Shapiro leaves it to the reader to judge whether the attacks of the "Roim" crossed the line into "jealousy and hate". I refer the reader to Toledot Mishpachat Rosenthal by Y. Y. Greenwald and I think it will be obvious that the reprehensible actions of the Roim against Shir' attempt bid for the Rabbinate in Prague certainly crossed the line into jealousy and hate.
2- pg. 3 note 11 - Shapiro mentions R' Yaakov Kamenetsky's view that the first four chapters of Yesodei Torah are not to be regarded as Torah. (Cf. the similar statements of Shadal - Devarim 6,5.) R' Yaakov expands on this view in Shai L' Melachim to Melachim 1 6,2 (My sincere thanks to R' Nosson Kamentsky for providing me with a copy of this booklet).
This excerpt from a speech given by R' Nosson contains the backstory behind this view of R' Yaakov:
"Beyond that, RNK said his father would have taken issue with the entire idea of denying the validity of modern science when it seems to contradict Torah as interpreted by Chazal. He recalled how R. Yaakov watched Neil Armstrong land on the moon (in the house of a neighbor who owned a TV) and conclude that, clearly, the first few chapters of the mishna torah that discuss the moon being a living spiritual being must have been based on Greek philosphy that had been conclusively disproven."
Not everyone, took this so sanguinely. The Lubavitcher Rebbe in one of his letters (quoted and critiqued here) makes a rather "violent" attempt to explain away Maimonidean astronomy and R' Shakh is also know to have commented that even Maimonidean astronomy is infallible (Update: I was referring to this, which for obvious reasons might not be the best example.) (Also somewhat relevant is R' Kook's Maamer Meyuchad - printed in the back of Toledot Yisroel of Ze'ev Yaavetz V. 13) [Update: See this comment for a similar view.)
pg. 11 n. 54 - Shapiro refers to the famous letter to R' Pinchas Dayan in which Maimonides admits to forgetfulness. In Mivchar Ketavim (pg. 120), R' Matisyah Strashun points out that in that case the Rambam didn't actually forget the source. (See here)
pg. 54 - In his list of scholars who trie to answer the Rambam in a way different then the Rambam himself answered in his responsa, Shapiro misses a major source. In the Kesef Mishna to Kriat Shema 1,8 , Maran throws up his hands in despair at one of the Rambam responsa to Chachmei Lunil and offers his own explanation instead.
pg. 57 n. 239 - Emendations that ignore the commentary to the Mishna. See this post for Rambam Berachot 1,15 in which most of the answers (including that of the Gra) ignore the explict statement of the Rambam in his commentary to the Mishna.
pg. 85 - On the Rambam and the Zohar - the Kesef Mishna (in Sefer Ahavah, I can't find the exact place right now but it should be easy to find with a DBS search) cites a Zohar as a soiurce for one of Rambam's halacha. I am not sure if he believed that the Rambam actually had the Zohar.
pg. 89 n. 376 - although not directly related to the book 'd like to mention an interesting source re: Rashi and Kabbalah. Rashi Beitzah 33a cites a Piyut Yotzar from one of the Chachmei Lombardy. The Gilyon writes that this is actually the Pirush to Sefer Yetzirah of R' Shabsi Donnolo (Rashi cites this Pirush- called Chakomini -in Eiruvin 56a). Possibly by Piyut Rashi refers oi the rhymed introduction. S. Y Friedman pointing to this example says that Rashi's language "I heard" means he heard it recited in the shul - which is unlikely if he refers to the pirush to Sefer Yetzirah.
Last essay - On the Rambam and superstition - I believe C. Tchernowitz in his Toledot HaPsoekim alsio provides some examples of the way in which Rambam phrases things to fit with his philosophical beliefs. (See note 4 here for a case where the Rambam phrases a statement to avoid an apparent anthropomorphism (this was already noted by Prof. Twersky, along with some other examples in the Chapter on Law and Philosophy in his Introduction) )
[1a] The Aderet produced many seforim on some rather unusual topics. They have only recently started publisihng them. I believe his is the only sefer in history that contains an approbation by the author to his own work, the kuntres Acharis Ha-Shanim on Vidui Maaser. Here are photos of the title page and Haskamos:
 See for example Ishim V' Shitot - R' Meir Simcha, as well as many of the reviews in Seforim V' Soferim. His review of Kasher's Rambam V' Mekhilta D'Rashbi has some particularly important methodological observations.
 Shapiro collects all his statements on the subject in the Hebrew section. I would add to his list the SE's statement in his responsa on abortion that R' Chaim's answer there, while brilliant, doesn't reflect the historical Rambam.
 See this post for a relevant statement by the Maharsha.