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There was one relationship I've been concerned about at the emotional level, however I really don't think anything is going on. She obviously hasn't admitted to anything like that.

If you read on this board and especially the others, you will be amazed by how many people in exactly your situation were "nearly sure" their souse was not having an affair, only to find out they were wrong. Let me repeat: until you rule it out 100% you are wasting your time trying to fix the marriage or even trying to get her to talk about it.

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One of our problems is that we've never really been able to discuss our relationship mainly (IMO) because she gets too defensive and starts reading personal judgments into things. Typically anytime we get into something that matters to me, she'll shut it down with something along the lines of "I know, I'm terrible/horrible/awful..."

Don't let yourself be derailed so easily. If she says that, just respond, "I'm really sorry you feel that way. Now can we go back to discussing the problem I brought up?" Pushing your wife to talk about an important topic even though it makes her feel bad does not make you a bad person. Bad feelings are not such a big deal. They pass. We all have them, and we survive them. If the issue is important to you, keep bringing it up. if she reacts badly, empathize with her, but don't back off. If she absolutely refuses to talk about it, that's her right. Then you have to decide whether you owe it yourself to be with someone else.