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Sounds like you're the unfortunate rebound boyfriend. I hate to say it, but I agree with the above poster.
There's a moderately good chance she's thinking about how she can get rid of you and convince her ex to get back with her. I hate to plant paranoid thoughts into your head, but it seems like she deserves the mistrust.
Whatever you do, you need to do something. Your avoidance of the issue is bringing on paranoia and is just going to push her away from you.
Clearly, she didn't think she was doing anything wrong if she asked you to read her text message to her. People who feel they have something to hide don't generally offer up opportunities to get caught. What you consider flirty may just be part of her personality. Flirting does not mean she doesn't care for you, and it certainly isn't proof that she's going to cheat on you or leave you. People go away to college and get homesick. That may well be all this is.
You have to tell her you know about the deleted messages. You have to ask her what her intentions are. And if you are really, really concerned about her maintaining a friendship with this guy, you have to ask her to let go of her past so she can focus on the present.
If you do nothing, the cycle will repeat.