The first and last pieces are from the Yaavetz' hagahot to Teshuvos HaRambam printed in Sinai (85) by A. Bick-Shauli. (Although Bick's work is unreliable, it certainly is not fraudulent as Goldstein claims in his discussion in Zoharei Yaavetz in Ohr Yisroel. Every example Goldstein quotes is simply carelessness and nothing more.)
The middle piece is taken from Hagahot Yaavetz to Sefer Me'or Einayim -Kovetz Tiferes Mordechai V. 3 (My thanks to Andy for lending me his copy of the sefer). Hence the reference to הבלי סודותיו.
N.B. Has anyone heard of a 3rd part of Mitpachat Soferim discussing R. Emden's "thesis" that the Moreh Nevuchim wasn't written by the Rambam (He discusses this a bit in part 2 but promises to deal with it at length later.)