Ok, I got a few things to say...
Seems kinda hinky that you are one who puts your heart and soul into the relationship and works to fix problems as they present yet you wanted to help her get back on her feet, financially speaking. Obviously, you seem dedicated, which makes me think she dumped you. So probably not a spur of the moment decision for her. What I do not get is why you still wanted to help her through school and support her. Most people would be pissed off in your case.
Does she have access to your house, such as a key? Did you change the locks when you separated? I doubt she was nice up to the day you separated, then just turned total bitch like that. Had to have been warning signs. Not blaming you, just sayin'... Plus, when she left you, she probably had some support system to keep her off the streets, unless of course she is an idiot.
If she did have access to your home, she could have simply logged into your computer and pulled up your bank account sites from your browser history. If you have the browser save your passwords it would be simple to get into your bank account information. Also, if you use the same passwords for everything, it would be easy to figure out your account information and then just enter your commonly used password.
I would do a few things in your case. Make a police report. Secure your home and possessions. Find out when the money was moved to try and prove you were not the one who made the transfer. That may at least prove to your bank you did not take the money and may be a way to get a return of some of the money. The other thing, find out which bank account it was transferred to. If it is an account in her name, seems like a sealed deal. Hiring a lawyer may not be a bad idea either.
I hope are not taking my comments as accusing, just rather offering my perspective from what you wrote to maybe help you learn. It sounds like a crappy situation. I hope you can get some of the acute issues resolved. I also hope that you can learn from this experience, grow, move on, and find a healthy relationship for yourself.
Good luck bro !