I'm not a native English speaker but I would say "so are we friends now?" because the auxiliary verb, that is "are", should be before the subject(we) and normally at the beginning of the phrase. The "so" sounds really strange and unusual being at the center of the phrase, because it sticks together two phrases. Also, "from" is unnecessary but I'm not that sure of it. Just because, I'd rather not use it.
I repeat that I'm not a native English speaker so there may be something wrong