As someone has already noted there seems to be a general lack of information on Shir. His position as a son-in-law of the Ketzos HaChoshen, as the Founder of Chochmat Yisroel in Galicia, and Chief Rabbi of Prague is enough by itself demonstrate the complexity of his position.
There is simply a massive amount of Shir's writings available on the Internet. These include:
1- Harkavy's Zichron La'Rishonim - These contain the first collection of letters between Shir and Shadal. (Artscroll released a book called Zechor Yemos Olam containing all sorts of correspondance between Harkavy and the Rabbonim of his day.)
2. Igrot Shir - and this contains the rest of the letters. This collection focuses on the argument on the origin of the Masoretes (Bavel acc. to Shadal, Eretz Yisroel acc. to Shir), a long commentary of Shir's to "deutero"-Isaiah (towards the end), Onkeles vs. Aquilas and other such issues. The volatile nature of their relationship is discussed (though not particularly well) in the Shadal bi-centennial volume.
3. Tochacha Megullah (the last part is in Hebrew)- This was Shir's response to the Reform convention in Frankfurt.
4. Toledot Mishpachot Rosenthal - This contains a good many documents relating to Shir's problems in Tarnopol and his attempt for the Rabbanus in Prague.
5. Otzar Nechmad - In the chapter on Tekufos Sa'arah B' Chayei HaChatam Sofer. Same as before.
6. Nachlas Yehuda - This was published posthumously by his son. The first part (Ner Mitzvah) is a letter to a friend of his who had become attracted to Chassidus. It's quite typical of anti-Hasidic polemic if its time. (Or says Barzilay whose work I will discuss soon. Unfortunately the file is missing pages so I acn't read the whole thing.)
The second part (Ohr Torah - a pun on the name of Geiger's book - Ur - schrift) is a very heavy attack on Geiger's magnum opus - "Urschrift und Übersetzungen der Bibel in ihrer Abhängigkeit von der innern Entwicklung des Judentums” (Basically - Original text and translations of the Bible as they relate to the inner development of Judaism - See Susannah Heschel's book on Geiger and the Jewish Jesus Ch. 2 for an overview. Basically he uses the Targumim to construct his own version of Second Temple history in order to support his own program of Reform (but don't worry its all very objective and "scientific"). Incidentally some of Geiger's works are also available in the same place.)
7. Lots of his ontroductions to various books are available, each containing all sorts of information - Shoresh Davar, Maamaer HaYichud (of the Rambam), Gal Ed (R' S. has already pointed this one out.), Higayon HaNefesh and (not on-line at the moment) Teshuvos HaGaonim ed. Lyck and the dictionary of Ibn-Parchon.
8. Kiryat Sefer Years 1-4 - M'Arkiono Shel Shir by B. Dinaberg containing some letters written by Shir