Hi Shauna,
Wow girl, very intense situation your going through. I concur with many of the previous posters about preparing for the worst, hoping for the best. I only wish I'd heeded some of that very logical advice in my own dealings with a disgruntled soon-to-be ex spouse.
I'm in a very similar boat right now myself although maybe a little farther along. My wife will have absolutely nothing to do with me transitioning or even dressing as my true self in our house with our daughters. Although she'll openly blast me with any negative expletive or slur you can think if without second thoughts. We've concluded we'll be divorcing, so it's a matter of when not if for us.
My wife has threatened the whole outing me to our friends and throughout the community we live, but she won't because it's her embarrassment and she knows I won't care, so that makes her even more infuriated with me. It would be the weight off my shoulders so to speak. She's tried the whole biblical thing with a pastor and it didn't work either.
Like yours, my wife has also gone thru my phone and iPad (both now have pass codes), she gone thru my personnel laptop, done web searches and she's found her share of pictures, emails, blog and more. She's even found receipts for clothing and counseling sessions ..... all of which she believes will be useful in divorce court. What she doesn't understand though and won't take time to learn about either is that being transgendered is not a crime and has little impact in divorce proceedings, at least according to some of the legal web searches I've done .... I'm sure it varies by state though (I live in Minnesota and there are some actual reported cases from here with positive outcomes, so I feel good about that).
What I would suggest is prepare for the worst .... Get your ducks in a row, do your research, keep a log of events between you and her such as things said, dates of altercations, etc.
Good luck dear!