What is the significance of the Pasuk "va'Yavo Moshe b'Soch he'Anan"?
Rashi: The cloud was a sort of smoke, and Hashem made a path for Moshe to pass through it.
What was the significance of the forty days?
Seforno: This corresponds to the forty days that it takes for a newborn baby to form 1 (and explains the forty days that Moshe spent on Har Sinai each time he ascended it). Here too, Moshe was being formed into a new being who was able to learn from Hashem what nobody else was capable of.
This symbolizes a higher plain (a rebirth) that Yisrael were destined to attain, were it not for the sin of the Golden Calf. Refer to 20:21:1:3*. They lost it during Moshe's first ascent, and Hashem was still angry during his second ascent. The third time they regained it to a degree, as the Torah testifies when it describes in Shemos (34:2) how his face shone (Seforno) - which Yisrael finally merited (Seforno). This also explains why the Torah only discusses the Mishkan following Moshe's third ascent, and why Aharon and the Levi'im were chosen only after the sin of the Golden Calf (See Seforno).
Moshav Zekenim citing a Midrash: During the day Hashem taught to him written Torah, and at night, Mishnah. 1
Moshav Zekenim: The angels say Kadosh Kadosh Kadosh... during the day, and Baruch Kevod... at night.
Why did Moshe need to know when it is day, and when night? Perhaps it was to recite Keri'as Shma, i.e. in times he was given between learning different Parshiyos. (PF)