Why should they distance from the Aron?
Rashi: It is due to Hashem's honor.
Ralbag (3), Malbim: It is in order that everyone will be able to see it.
Why does it say "u'Veinav" (plural)?
Rashi #2: There were two Aronos
Why were they about 2000 Amos from the Aron?
Rashi, citing Tanchuma: It is [within the Techum of 2000], so they can go in front of it to pray on Shabbos. Hashem knew that they will besiege Yericho on Shabbos. 1
Radak: This is why it says "ba'Midah" with Patach under the Beis
What is "l'Ma'an Asher Teda Es ha'Derech"?
Rashi: This is why you go in back of it (to know which way to go).
Radak: It is lest you enter mixed up. [Rather,] you will see the Aron from afar, and go straight, in back of it.
Malbim: It is distanced in order that everyone will be able to see it and follow it. The Asnachta on "ba'Midah" supports this 1 . According to Rashi (this is why you go in back of it), the Asnachta should be on "Elav".
I.e. 'do not come close' is read together with 'in order that
What is "Ki Lo Avartem ba'Derech
Rashi: You did not go like this until now. Radak
Why does it say "k'Alpayim"?
Radak #1: The Chof is of Shi'ur (about 2,000)
Radak #2: The Chof is of comparison. The distance is like the distance you should separate when we camp in front of Yericho, so you will be able to come to pray in front of the Aron on Shabbos.