What did Hashem mean when He said "Peh el Peh Adaber bo"?
Rashi #1 and Targum Yonasan: He meant that He specifically instructed Moshe to separate from his wife. 1
Rashi #2 (in Iyov, 4:12): This can be compared to a man who had a wife and a concubine. He came to his wife he came openly, but to his concubine, he came secretly. So too Hakadosh-Baruch-Hu, regarding the prophet of the Nochrim, the Torah describes how He appeared to Avimelech 2 and to Lavan 3 in a dream of the night; 4 Whereas by the Nevi'ei Yisrael, the Torah writes "Peh el Adaber bo."
Ramban: He meant that when He spoke with Moshe, He spoke with him mouth to mouth - and not in riddles.
Seforno: It means that Hashem spoke with him with the Name Hashem, whilst he was awake.
What was Hashem referring to when He said "be'Mar'eh ve'Lo be'Chidos"?
Seforno: Bearing in mind that the other prophets received their prophecies in the form of riddles 1
Seforno: Some of which required assistance in solving
And what is "u'Semunas Hashem Yabit" referring to?
Rashi and Ramban (in Pasuk 6, citing the Sifri): It is referring to when Moshe saw the back of Hashem's Tefilin. 1
Seforno: It repeats that all of the above advantages of Moshe's prophecy over that of the other prophets were added to the fact that he prophesied with the Name of Hashem.
Why does the Torah write "be'Avdi be'Mosheh"?
Rashi: Hashem was pointing out to Aharon and Miriam that they would have had no right to speak of Moshe derogatively even if he had been an Eved Hashem who was not Moshe or Moshe had he not been the Eved Hashem; 1 how much more o now that he was both.
Even had Hashem not designated Moshe to be His Eved, he would have been a very special person.
What did Hashem mean when He said "Madu'a Lo Yereisem ... "? Why ought they to have been afraid to speak against Moshe?
Seforno: Refer to 13:8:6:1.
What is the significance of the fact that Moshe was Hashem's Eved in this context?
Rashi and Seforno (on "Madu'a Lo Yereisem ... "): Irrespective of who the Eved Hashem is, Aharon and Miriam ought to have known that Hashem would not display His love for someone who was not worthy. 1
Rashi: And to suggest that Hashem was unaware of Moshe's deeds (and that they knew what Hashem did not - Seforno) is even worse!