Sold on Ebay (it will be interesting to see what other letters the seller has):
On Lilenblum - see here and here.
You can find other letters on Ebay with this search. (If anyone finds anything interesting please leave a comment.)
Also see here for links to several editions of R' Yaakov Emden's Mitpachat Seforim - Part 1- on the Zohar, Part 2 - hasagot on Aviad Basilea's Emunas Chachomim (tirade against Ibn Ezra, Ralbag and anyone else the author doesn't consider frum enough.)
(Does a Part 3 exist -devoted to the Rambam and MN?)
This edition is the most readable but it only has Part 1.
One can also find M. Kunitz's Bar Yochai attempting to refute R' Yaakove Emden's arguments. The book was almost universally disdained (R' Yosef Shaul Nathanson calls him a מפטפט in his hagahot to SA YD. Shir wrote a biting rebuttal that I described here). See Y. Y. Greenwald "Mekorot L' Toledot Yisroel" for more on Kunitz (he defends his connection with A. Choriner - my thanks to andy for this source).