You are spot on when you say that none of us are perfect, but, if we were to be perfectly honest, there are things about our partners that are annoying and wouldnt be missed.
Except anything about me, because, well, I am perfect. Haha - I crack myself up.
Anyway, I think it is inherent in two people living together for long periods, that there would be.
Part of this journey for me was to uncover the things about myself that I thought were annoying and to work on those. So, good on you for doing that.
As far as your wife, you are playing this exactly right. Sometimes I would literally sit back and watch my h's actions. It was amazing to see part of the real him and part of the "other".
Sounds like your w's gf touched a bit of a nerve. Not necessarily a bad thing. Good for you that you didnt respond and just let her talk.
I think your wife is swirling it all around in her head. Trying to get a handle on who she is and what she wants.