I just borrowed the recently published volume entitled Afikei Mayim, composed by a (seemingly close) talmid of Rabbi Moshe Shapiro, a Rabbi Schmeltzer, if I remember correctly. (I've returned the book already, and although I took some notes beforehand, I'm working partially from memory.) I read through the introduction and the first section of the book, which is called "Likut Kedushas Ha-Torah," and is mostly comprised of quotations from various sources that advocate what one might call a sort of "fundamentalist" approach to the Torah, the Talmud, Chazal, and the Rishonim. I was glad to read it, because it argues (thoroughly, I hope) for a perspective fiercely opposed to what I present in "Sources Indicating That Chazal Did Not Possess Perfect Scientific Knowledge." The examination of opposing views is an important part of any truth-seeking endeavour; counterarguments will either reinforce a prior opinion, if they prove weak, or change it in their strength. I personally found this book's exposition uncompelling.
I'd like to note a few thoughts I had while reading and pondering the book.
1. Regarding the question that most interests me – the quality (and quantity) of Chazal's scientific knowledge: I counted, in an informal tally, about 7 sources that clearly assumed that Chazal never erred in their scientific statements. Three of them were major authorities: the Rivash, the Maharal, and the Chazon Ish. Two others – the Gra and the Chida – seemed borderline to me; I couldn't decide whether they were definitely taking this position or not. The earliest of all these writers were the Rivash and the Rashbatz, who lived in the fourteenth century. All the rest were Acharonim.
One thing that struck me (as it has in the past) about many of these sources was that they were long on the hyperbole but short on the proofs. Very short. The argument, it seemed to me, generally went like this: "Chazal were unfathomably holy and close to God. We are mere dust at their feet. Anyone who questions them is going straight to Hell. [Insert biblical verse here.] All of those passages that seem to contradict modern science mean something completely different, much deeper and more sublime. What exactly do they mean? I haven't the foggiest – or – I can't tell you. Also, all of modern science is wrong, except for the parts that they stole from us. Chazal never made mistakes. They knew it all. Trust me." That, to me, is not a convincing presentation.
Sorry if you found that last paragraph a bit too biting for your taste. I do generally try to be judicious.
2. I was blown away by the quotation of the Rashbatz in a footnote (#3 or #4, I believe) which seems to aver that Chazal not only didn't make scientific mistakes, but actually knew all scientific facts. I am reluctant to believe that the Rashbatz really thought that Chazal knew everything in the scientific sphere; nonetheless, the quotation from him may lead others to that conclusion. I had started to believe that the fourth grouping in my post on the topic of Chazal's scientific knowledge – sources indicating that "Chazal Were Not Scientifically Omniscient" – was redundant, for nobody with any intelligence would ever contest the point. Now I'm not so sure.
3. Notice footnote #6: a quotation from the Shevus Yaakov that includes his insistence that the Earth must be flat, since the Talmud says so.
4. Perhaps there are some fine distinctions that I missed, but my impression was that some of the sources the book quotes (Rabbi Chaim Vital, for instance) advocate complete literalism in interpreting the statements of Chazal, while others (Maharal, for example), reject literalism in favour of... something else – though maybe not what would classically be called allegory. This does not constitute a flaw in the book; a compilation of views need not present one unified approach to a topic (indeed, variety is often good!). I'm merely pointing out that the book seems not to present a unified approach.
5. I was a bit confused by the author's reference in a footnote (I think at the beginning of the Kabbalah section) to the statement of Rabbi Yosef Shalom Elyashiv (whom he does not actually name) that "They were permitted to hold this opinion; we are not." When Rabbi Aharon Feldman cites this statement of Rabbi Elyashiv, he describes the context as follows: "[Rabbi Elyashiv] was asked: if he considers [Rabbi Nosson] Slifkin’s approach wrong how could so many earlier authorities have held it? He answered: 'They were permitted to hold this opinion; we are not.'" However, as presented in Afikei Mayim, Rabbi Elyashiv seems to have been discussing belief in Kabbalah. It would be nice to know who his interlocutor was when he made this comment. (Or maybe someone could encourage him to write a piece on the topic himself?)
6. I really liked the responsum stating that it is heresy to contradict anything in the Or Hachaim.
7. The author calls into question the authorship of certain letters attributed to Rabbi Shamshon Raphael Hirsch. I'll assume that Rabbi Hirsch was indeed the author, given that Rabbi Dr. Mordechai Breuer, who I understand to be a leading expert on Rabbi Hirsch, believes the letters to have been his (and, indeed, published them as such).
8. The author also calls into question the authorship of certain passages attributed to Rabbeinu Avraham ben Harambam. I know that Mossad Harav Kook – a reputable company – published Rabbeinu Avraham's Milchemot Hashem, containing what I assume are the incriminating passages. The book was edited by Rabbi Reuven Margolios, author of Margoliot Hayam, and the title page says, "Published from a manuscript written during the lifetime of the author." I believe, as well, that the famous (and recently controversial) excerpt from it has been printed in the standard Ein Yaakov editions for more than a century, without any great fuss being made over it by the bulk of rabbinic authorities. These reasons all lead me to assume that it is indeed authentic.
(Aside: I suspect that the authenticity of the Hebrew Bible could be subjected to challenges far greater than those confronting the work of Rabbeinu Avraham.)