inbetween,
You did a great thing and I congratulate you. It's not easy having those conversations. You never know when your witness spouse is going to take a minor conversation nuclear and have it spread to all sorts of topics and parts of your life that you didn't want or expect.
I have just a couple of ideas that may help you. You could, if you don't already, start using the word grace in your conversations. Don't go overboard but use it instead of other words that you may already be using. You know it's not a word or concept that Witnesses have so hearing the word is actually quite jarring to them at first. But, hearing it from you and never hearing it at the hall may help you in the long run.
If she wants to know the scriptures better ask her if she'd like to read the Bible together. Whether you use this as a chance to plant seeds or just read the Bible as a way to strengthen your connection is up to you. You could even follow the WTS schedule since she's probably wishing she could do that already. But, when questions come up or discussion arises you should use a non-WT book or commentary for research.
The other thing I thought of while reading your post was her loyalty to the Org.. I was thinking that before you show her how controlling the GB is and how they are not God's mouthpiece that you should set up a new foundation for her. Right now the GB and Witness structure is her spiritual foundation. No matter what happens she will cling to it. However, if you start mentioning how Christ is the real foundation for christians and how he is the head of us (without getting into the trinity quicksand with her) you can begin to set up a foundation next to hers and slowly move her over to it. You may need to do some advanced study on Christ and our relationship to him but there are excellent scriptures and some helpful books that can aid you.
Good luck.