Well you already know she's lied to you, the only question is how much.
All the stuff with the phone password changing and deleting of texts points to an affair, but the unfortunate truth is you'll probably never know.
All you do know is she's a liar, she's deceived you to a degree but you don't know how much and you probably never will.
About the only suggestion I have is that you take a hard line, and you tell her that with all the password protecting, deleting of text messages, and "trickle truthing" she's giving you, the only way you will rest easy is if she takes a polygraph test. If she declines, then well, she's gotta be guilty. If she accepts, you hope for what is known as a "parking lot confession" some time prior to the polygraph which is really the reason you do it because polygraph tests are notoriously unreliable but hopefully she doesn't know that.
For lots of guys that would be enough to walk away, others will find some way to accept/justify/rationalize her behavior and find a way to live with it, always wondering and always keeping "one eye open" because if it happened once it could very well happen again.
I'd like to think if it was me I'd just walk away but your mileage may vary. Especially with another kid possibly on the way. How the heck did THAT happen especially with all the problems?
Things are more like they are now, than they ever were before - Dwight D Eisenhower