You are correct that "so" is being used for emphasis. However, I consider this to be a bad habit of many young people, especially in the States. Our teachers do not teach us to speak this way!
I think that Rachel must be an enthusiastic young woman or teenager. Her use of "so" probably means that she is pleased or confident about the situation.
Please notice that "so" in this phrase is not necessary. "So" adds nothing to the original meaning of the phrase. "...I think we are on the right track!"
(We are either "on the right track" or not.) The phrase does not need any more emphasis.
About the use of "very":
No, it would not sound right to add the word "very" instead of "so". If I am required to replace it with another word, I would choose the word "definitely." (As in, "I think we are definitely on the right track.")
However, I think it is best to say, "I think we are on the right track."