Having already informed us in Sh'mos (17:1) that they were in Refidim, why does the Torah see fit to write here "Vayis'u me'Refidim"?
Seforno: It teaches us that they left Refidim with the express intention of arriving at Midbar Sinai where the Mountain of Hashem was situated, in order to receive the Torah.. 3
Oznayim la'Torah: Having interrupte their leaving between Refidim and their arrival at Har Sinai with the Parshah of Yisro and the judges, it needed to repeat that they arrived at Sinai from Refidim.
See Ramban's objection to the question. He therefore cites the Mechilta, which bases the question on the Pasuk in Bamidbar (33:15) which, in connection with the journeys and encampments of Yisrael in the desert, includes the one from Refidim to Har Sinai - so why 'repeat' it here?
Which they knew because Hashem had told it to Moshe a year earlier at the Burning Bush. See Sh'mos, 3:12 (Seforno).
Why does the Torah write "Vayavo'u ... " and not "Vayachanu ... "?
Ramban: So excited were they in anticipation of receiving the Torah,, that the moment they entered the desert and saw Har Sinai in front of them, they encamped on the spot, 1 without searching for a suitable location to set up camp. 2
Having just said "Ba'u Midbar Sinai", why does the Torah repeat it?
Ramban: Refer to 19:2:2:1.
Oznayim la'Torah: To reach us that they had defeated Amalek, who had come to prevent Yisrael from receiving the Torah, and that they were now ready to receive it. 1
See Oznayim la'Torah.
Why does it add the words "Vayichan Sham Yisrael"?
Ramban #1: To teach us that they separated the Eirev Rav from their midst. 1
Ramban #2: In order to mention them in a dignified manner when they came to receive the Torah.
Seeing as the Torah was given to Yisrael exclusively, as the following Pasuk clearly states (Ramban).
Why does the Torah write "Vayichan" in the singular?
Rashi and Targum Yonasan: 'Like one man, with one heart!' 1
In contrast with all the other encampments, throughout the forty years, which were performed with strife (Rashi, citing the Mechilta). Oznayim la'Torah: Because the only thing that unifies Yisrael and turns them into a nation is Torah and their belief in One G-d ('Yisrael, Oraysa ve'Kudsha-B'rich-Hu Chad Hu'). See Oznayim la'Torah who eleborates at great length.
Seeing as the Torah is mentioning the mountain for the first time, why does it write "Neged ha'Har"?
Oznayim la'Torah: Because it is the mountain known as :Har ha'Elokim", which Moshe told Yisrael aabout the mountain upon which Hashem had revealed himself to him, and on which He had commanded him to redeem them and bring them to Him and to worship Him on it.
QUESTIONS ON RASHI
Rashi writes that they left Refidim in Teshuvah. The Mechilta says that Refidim is an acronym for 'Rafu Yadayim' (they slackened from learning Torah), and this is why Amalek came!