1. This says:
שלומכם ושלותכם יסגא מאוד בני יניק וחכים כמר יהודה הנקרא ליב שיחיה לאורך ימים עם חבירך יעקב שיחיה עם שאר חבירים הש"י יגדלכם לתורה ולמעשים טובים
Which roughly translates to:
"Much peace to you all and all of yours my young and wise sons, like the Mr. Yehuda called Leib may you live till the end of days with your friend Yakov, may you live with the rest of the friends הש"י (not sure what this is), may you all grow in Torah and good deeds."
The RaMa then proceeds to answer a question about tefillin.
Firstly, please correct my translation if it is wrong. Specifically "כמר", which, because of the "כ", I understand this as the ReMa comparing his "sons" (the ones who asked the tefillin question) to a Mr. Yehuda Leib and his friend Yaakov.
Secondly, I'm not sure that בני in this context means literally "my sons" - it could be the same way a Rabbi today might call a young congregant "my son", or it might be the way a father-in-law today might call his son-in-law "my son" - but that would depend on other texts of the same era.
Thirdly, if the way this actually translates actually means the RaMa had a son named Yehuda Leib, it ALSO would mean he had a son named Yaakov.
2. This source roughly translates as:
"It is not clear to us based on what is written that RMA had four sons and a daughter. We know:
a. Rabbi Yehuda Leib.
b. Rabbi Shimon Wolf, died in Krakow on Wednesday the 6th of AV 5359 (July 28th 1599).
c. Mrs. Dresil The wife of Rabbi Simcha Bunim Meiselsh
d. Malca the wife of Rabbi Eliezer Leizer Ginzburg.
e. Mrs. Sarah, perhaps she was the one who married Rabbi Zvi Hirsch Tsuizmer."
Elef Margaliot was published in 1993 so not really a primary source, but I'm assuming that he put his own sources in his own notes. Can you see what he states as his source for "knowing" that the ReMa had a son named Rabbi Yehuda Leib and a son named Rabbi Shimon Wolf?
3. Roughly translates as:
"The sons of the gaon Moshe Isserles:
a. he had one son and his name was Wolf (note 17 - "understand that my source does specifically state that he is the ReMa's son because he had no other source, but it is understood from context". Also note 17 - "his name is the name for his nephew Rabbi Shimon Wolf, the father-in-law of the Sha'ch, great-grandson of the R'Ma"), the son-in-law of Bundil or Zundil of Kamenetz father of Rabbi Heschel of Krakow"
I think that the "Understood from context" is the issue here:
Maybe he's assuming that because the father-in-law of the Sha'ch (Rabbi Simon-Binyamin son Isaac Wolf Meisels, of Vilna) is the great-grandson of the R'Ma, that his uncle Shimon Wolf must therefore be the R'Ma's son or grandson. However, Simcha Simon Wolf is the great-grandson of the Rema through his mother's (Leah Bunim Meisels) mother (Dreizel (Therese) Bunim-Meisels).