Is this sentence correct?
Not having been to America before, it was an entirely new experience for her.
Shouldn't it be (for example):
Not having been to America before, she was struck by its uniqueness.
(in this case the subject is the same in both parts of the sentence)
What's the correct version?
Technically, you are correct. The "it" is in the position that "she" should be in.
Although technically a misplaced modifier, few people would fail to understand.
You changed the meaning though: "it was an entirely new experience for her" does not mean the same as "she was struck by its uniqueness"
You could say "she had an entirely new experience."
Or you could rewrite the first part instead: Because she had never been to American before,...
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.