Sounds like you really want to save this marriage for the sake of your family. In that case, you need to bust up this recent EA. She's withdrawing likely because she's taking it underground and probably doesn't feel guilty since she's justifying it with your past EA.
You need to expose and get her to send a no contact letter to the OM. Does she work with him? If so she will need to leave that job.
You will not be able to repair your marriage fully until you address the EA and get rid of the OM. Your wife needs to end all contact so she can grieve and move forward with you and work toward recovery with you. Until that happens, your marriage will continue to be in limbo and she will withdraw and come out of her shell only often enough to make sure you're still her fallback. Is the OM married? He likely has no intention of leaving for an EA and your wife knows this. Exposure will make him run.
I have accessed her phone without her knowing and have gone through everything, every app, every message, everything. I'm seen texts with friends talking about the whole situation in detail and I have not seen anything that tells me things ever became physical or that she is still talking to him. We had a small argument last week over something and I had asked her again if she was still talking to him and she told me no, and that whatever I said to him when I confronted him scared him to the point of cutting all contact with her. Whether I fully believe that or not is a whole other thing, but from what I can see there has been no contact. So at this point I need to just take all this as just an unsolicited text as she's told me it was and as I've seen she's told all her friends it was.
That being said, we did speak briefly about things yesterday. She noticed something was bothering me and asked me what, so I told her. I told her that I feel like I don't know what direction we're going in or even trying to go in and it bothers me. I told her that which ever direction we go in at this point is ok, but let's make a decision and make it known to each other and go with it. She said to me "You make it sound like the easiest decision in the world". I said no, the easiest decision in the world would be to just say F it and walk away from it all. But I'm not ready to give up fighting for us and the life and family we've built together because of a couple bad years and a few stupid choices made by both of us. And she told me that she couldn't make a decision yet and that she needs to feel comfortable right now and at peace with things.
Now yes, I understand this to an extent. I have seen things and jump to conclusions and made accusations, right or wrong I did it and it made her feel uncomfortable that I'm constantly watching her and I don't believe a word she says. In the past week she has done things, said things, and asked things purposely trying to piss me off and react, but I didn't. I've realized that she's testing me, she's trying to see if I'm going to flip out over any little thing like she's said I've done in the past. I know I've done it and I'm conscious to it now so I'm trying my best not to do it.
Will things get to a point where we can really rebuild? I don't know. But for now I just have to keep a watchful eye and see how things progress. It's not worth letting all the little things get to me and make me upset. If things get better great, if I find something that proves 100% she's been lying this whole time, then it's over.