Yes, the childhood issues, among other things are what we refer to as FOO issues (Family of Origin). Pretty much everyone has some sort of FOO issues going on in their lives. Some are big, some are small. And yes, it absolutely sets the tone for what you do with your life, how you handle things. The deal is, that many of us don't realize this until we implode with the whole A thing. That's what it takes for some of us to finally get it and start doing something about it.
Here's where it gets tricky in my opinion. You have trust issues. Yes, I know that one of the main things that we read here on SI is about trust issues when it comes to a BS trusting a WS. But there is another aspect to it. The WS has to learn to trust their BS, mostly when it comes to R and communication.
Your BS knows you probably better than anyone else. It sounds like she is giving you ideas on what you should be doing and giving you opportunities to talk with her. Trust that she wants this and that she can handle whatever you have to say. Trust that she isn't doing this to treat you the same way as your family treated you when you were young. Trust that she is doing this because she loves you, even if she hates what you've done.
On the eye contact thing...don't worry so much about it right now. Rather, next time you two talk, sit knee to knee facing each other. Promise to not move away. Just sit close, actually touching knees. It will feel weird, but it will change your communication a bit.