[A continuation of the earlier series - here, here, and here.]
One of the most interesting, unexplored aspects of HaRav Shir’s legacy is his policy of inclusiveness and tolerance [1a]. Since this particular belief influenced some of the most important episodes of his life, and indirectly, the future of all Jews, I’d like to discuss this at some length.
It is necessary to give some background in order to fully understand the significance of this opinion of Shir. As it is clear from the first part of his Nachlat Yehuda (and from other letters), Shir had no great love of Chasidism. He believed as did most of the Maskilim of his time, that Hasidism was an unhealthy sort of cult. This was reciprocated by the Chassidim who by all accounts made his life in Tarnopol a misery, even to informing the Government that he lacked a proper marriage license [1b]. He may have been placed in Cherem earlier in his life . See B I believe that this personal experience with religious intolerance might have contributed to the development of his view.
The most complete exposition of Shir’s “policy of tolerance” is in the Zikhron L’Achronim by A. Harkavy , pgs. 43 – 49 (pg, 360 – 354 of the pdf). I will try to recap some of the major points of the letter  here.
1.- Shadal in various places had, in turn, attacked I. M. Jost , Ibn Ezra and Rambam. Shir had responded to Shadal’s attacks in his letters. Shadal writes that if Shir champions an deceitful personality like the Ibn Ezra that doesn’t reflect well on Shir himself. Shadal points to the perils of heresy to the Jewish people as the reason for his sharp opposition.
2 – Shir responds that his love for the Jewish people is as strong as that of Shadal, and it is that very love that lies behind his own position of tolerance. Who is he that he should try to look into the hearts of his fellow man and judge them? How can he tell them that he, and he alone, knows the right path that must be followed?
3 – Men have often thought up new heresies but they were quickly forgotten in the depths of time. The zealous (Kannoim) however can cause real damage. Shir points to the destruction of the 2nd temple as a result of misplaced zealousness [2a]. If each man must divide himself from everyone else who thinks slightly different then he does then the Jewish people would be split into a multitude of small groups (he points to the numerous groups of the Chassidim as an example of this.) Such division within the Jewish people is a far greater problem then any heresy.
4 – He points to the opposition against Mendelssohn, and Wessely , the French Rabbis against the Rambam who also believed they were removing heresy but caused only destruction. He points to the Ramban's "תוכחה מגולה ואהבה מוסתרת" as a better method of reproof.
5 - Shir asks if Shadal considers the religious zealousness of the Crusaders, who killed whole communities without mercy in their pursuit of heresy praiseworthy. What harm can heresy, which is merely in the minds of the few men, and was always ignored by the masses do in comparison? On the other hand, asking question even if they sometimes result in heresy more often lead to a truer and more complete belief (pointing as examples to Saadyah Gaon's Emunot V' Deot, Chovot HaLevavot and Moreh Nevuchim as examples).
6- He writes that the spirit of the times is against intolerance (America and Europe -Locke and Jefferson, I assume) and that the age-old hatred of those with differing beliefs cannot and will not continue.
This is the basic outline of this fascinating document although the original should be consulted as I have left out many important details. In the next post, I will discuss how this belief of Shir's influenced his relations to R' Zechariah Frankel and Samson Raphael Hirsch.
[1a] See also G. Perl – “Pluralism and Tolerance in the works of the Netziv” TuM Journal, and T. Ross - “Between Metaphysical and Liberal Pluralism: A Reappraisal of Rabbi AI Kook's Espousal of Toleration”, AJS review.
[1b] This is recorded in KS 1 – B. Dinaberg “M’Arkyono Shel Shir”. It is not clear there if this was done by the Chassidim but since they were his opponents I am assuming that is who it refers to. Toledot Mishpachat Rosenthal has some letters relating to that period. Interestingly, see the letter of the Minchat Eliezer (Munkatch) printed in the back of Greenwald’s Otzar Nechmad – I am not sure what he is referring to.
 See wiki - the exact nature of his difficulties with the Yeshuos Yaakov is unclear. See Bernfield, Toledot Shir, but see the pamphlet L' Toledot Shir - published by P. Wettstein
 On the stormy relationship between Shadal and Shir see – Shmuel Werses, “Shadal and Shir: Luzzatto and Rapoport through their letters” – Samuel David Luzzatto bicentennial volume. On their polemics as they relate to the Ibn Ezra specifically, see A. Weiser, “The controversy surrounding the Ibn Ezra in the works of the Haskalah”, Sinai 61 and S. Vargon, “The dispute between Shir and Shadal regarding the Ibn Ezra...” Morashaseinu 10 (expanded version in the bicentennial volume) and see S.'s post here. The best biography of Shadal remains that of M. Margolies, which discusses many of the issue mentioned in this letter.
[2a] Misplaced zealousness is an important topic in R' Yaakov Kamenetsky's thought as well. See for example Emet L' Yaakov to Bereishit 49, 7 and many other places.
 See the sources mentioned in this post.