One such question relates to verse 2:
What does שְׂאוּ mean?
ב שְׂאוּ, אֶת-רֹאשׁ כָּל-עֲדַת בְּנֵי-יִשְׂרָאֵל, לְמִשְׁפְּחֹתָם, לְבֵית אֲבֹתָם--בְּמִסְפַּר שֵׁמוֹת, כָּל-זָכָר לְגֻלְגְּלֹתָם.
'Take ye the sum of all the congregation of the children of Israel, by their families, by their fathers' houses, according to the number of names, every male, by their polls
Could it mean "count", a logical translation of the word, given its context?
Such a translation would be deeply problematic, because the Torah specifically warns Moshe against counting the nation, and he has to do so only indirectly, through each person's donation of half a shekel.
יב כִּי תִשָּׂא אֶת-רֹאשׁ בְּנֵי-יִשְׂרָאֵל, לִפְקֻדֵיהֶם, וְנָתְנוּ אִישׁ כֹּפֶר נַפְשׁוֹ לַיהוָה, בִּפְקֹד אֹתָם; וְלֹא-יִהְיֶה בָהֶם נֶגֶף, בִּפְקֹד אֹתָם
'When thou takest the sum of the children of Israel, according to their number, then shall they give every man a ransom for his soul unto the LORD, when thou numberest them; that there be no plague among them, when thou numberest them.
There is also a 3 millenia-long tradition in Tanach against counting the nation, and in more recent times there has been a Halachik discussion regarding if and how one can take a census of Jews.
So translating שְׂאוּ as "count" is a problem.
The earliest occurrence of a word in the Torah with the same route is found after Cain's offering is rejected by God. In Genesis 4, he is told:
Not only does the word here refer to being lifted up, it also refers to being lifted up in the context of man's actions.
ז הֲלוֹא אִם-תֵּיטִיב, שְׂאֵת, וְאִם לֹא תֵיטִיב, לַפֶּתַח חַטָּאת רֹבֵץ; וְאֵלֶיךָ, תְּשׁוּקָתוֹ, וְאַתָּה, תִּמְשָׁל-בּוֹ.
If thou doest well, shall it not be lifted up? and if thou doest not well, sin coucheth at the door; and unto thee is its desire, but thou mayest rule over it.'
So how does this relate to Numbers 1:2?
The Ramban offers a fascinating insight from the Midrash which relates the word שְׂאוּ to Joseph's time in jail, and the story of his interpretation of dreams. There, Joseph tells Pharaoh's butler that he will be raised up (reinstated) to his former position, but that the baker's head will be raised up (hung) on a tree. The word used for both scenarios has the same route as שְׂאוּ
יג בְּעוֹד שְׁלֹשֶׁת יָמִים, יִשָּׂא פַרְעֹה אֶת-רֹאשֶׁךָ, וַהֲשִׁיבְךָ, עַל-כַּנֶּךָ; וְנָתַתָּ כוֹס-פַּרְעֹה, בְּיָדוֹ, כַּמִּשְׁפָּט הָרִאשׁוֹן, אֲשֶׁר הָיִיתָ מַשְׁקֵהו
within yet three days shall Pharaoh lift up thy head, and restore thee unto thine office; and thou shalt give Pharaoh's cup into his hand, after the former manner when thou wast his butler.
יט בְּעוֹד שְׁלֹשֶׁת יָמִים, יִשָּׂא פַרְעֹה אֶת-רֹאשְׁךָ מֵעָלֶיךָ, וְתָלָה אוֹתְךָ, עַל-עֵץ; וְאָכַל הָעוֹף אֶת-בְּשָׂרְךָ, מֵעָלֶיךָ.
within yet three days shall Pharaoh lift up thy head from off thee, and shall hang thee on a tree; and the birds shall eat thy flesh from off thee.'
Here we see that the word יִשָּׂא is used in two opposite contexts, both relating to the subject's actions.
So, does the Torah use the word שְׂאוּ to mean count, or is there a deeper meaning attached to the word?
Perhaps 3 key stories in the book of בְּמִדְבַּר can point us towards an answer: the stories of the spies, Korach, and Aaron and Miriam relate to examples of dissatisfaction and egotistical rebellion against Moses, that all end in disaster. These stories warn readers against the destructive potential of such hollow behavior.
In using the word שְׂאוּ to describe the nation numerically - the Torah's message seems to be that numbers in-and-of-themselves are not the true measure of potential. Rather, we can achieve our potential - whether it means to be raised up for the good, or for the bad, depending on our actions.