つまり... 目が覚めたら突然女の子になっていた... という事でいいですか?
In other words... when you woke up you had become a girl... is that correct?
Why「なっていた」is used here? He became a girl and he hasn't transformed back to a boy yet. It is supposed to be「なっている」based on my understanding. Is it an error?
They are talking about a experience that happened in the past, if you use 「なっている」...
If you're asking if the negative form of the verb 逸らす would also affect 合わせる, it would not. "To make eye contact and not look away" is correct. If you want both to be negative, you would have to say "合わせないで逸らさない" (although, it makes no sense in this context).