Whew, this is going to be a long one. I hope it will help you.
You know this is not going to be easy. Your W and OM being at the same work place is going to make it THAT much harder. It's the small things, those small things those OM do that made us feel good at the time. Even if he winks at her, or calls her "babe", or says a code word, or makes a joke only they would understand together....all those things can happen on a daily basis. All those things make her second guess her feelings toward you. She thinks, "HE never did that with me, HE never called me that, HE never makes me laugh, ....I must NEVER have loved Stuck!"
I hate to tell you this, but I think the affair is ongoing. If she says she is "separated" that means she is still having an affair or wants the "ok" to have an affair. She thinks if you would ever find something out, she would be able to say, "Well, I TOLD you we were separated!!!!!" I stayed in the bed with my H until the OM told me that it was not right and basically got mad and made me kick him out. I know...the whole thing is sick.....
There's lots of reasons that she could be stalling the divorce. The one you have to hope is a "top reason", is that she is still unsure about your relationship and whether she wants to leave you. But, she could be stalling because of finances or something the OM needs her to wait on.
During the affairs, I was just evil to my H. I was angry at him all the time, and tried to be away from him most of the time. In between affairs, I was sad. Sad that my H seemed to not be able to compare to the OM. I just kept thinking how "OM1 would have done this ...and he would have done that...." and my H does NOTHING!!!! Anger!!! In fact, if he would get that sad look it would PISS ME OFF!!!! After the last affair, when I confessed to H, and we said we would try again, I was extremely depressed. Nothing made me happy. This OM drug was gone and I was left with a H that didn't meet my needs. We had soooooo much to work on, and it was depressing. EVERYTHING reminded me of the OM. EVERY DAY. I slept a LOT, laid down A LOT. My H let me. DIdn't get mad. It was something I had to get through, and he knew it. I questioned whether I made the right decision. I prayed. I confessed my sins. I laid some more.
Initially, when I recommitted it was purely on faith, and the fact that I did not want to have my son part time. I couldn't bear the thought of it. I depended on this forum a lot.
I know what your wife is feeling. I thought what she thought: "it's either there or it isn't". I don't think that anymore. I realize that my love now for a person would of course be different than the love I had when I met my H those many years ago. I am 13 years older than I was back then. Obviously, I have matured and know and feel things that I didn't know and feel and need before. That's where she is wrong in her thinking about these new feelings she has. Unless she wants to continually change partners every few years, she will need to grow with you. Sure, if she doesn't mind changing partners, she can find someone better than the one before each and every time because as you grow sometimes your needs change. THe key to marriage is growing with your partner, committing to that growth. Would she want a partner that gives up on her and leaves her every few years to find a better wife rather than work at it together?
As for getting those feelings she needs. It is going to take work, a lot more now that she had the affair. And, more than anything, TIME. TIME is the biggest thing. She can't expect that those feelings are going to come all of the sudden. She needs to see the difference between beginning love and mature love.
She may only have her mom and sister who are not supportive of marriages, but at the beginning I only had my egf. So, don't think it is not possible. SHE needs to educated herself on affairs and love and marriage. SHE needs to realize things. HOw? That's for you and GOd to figure out. There are lots of ways to do this.....talk to her yourself, get her to go to Retrouvaille, a counselor, have a close couple talk to her, get someone that had an affair from your church talk to her. Pray. Meanwhile, you work on yourself. Work on those things that she has always wanted you to do. If it is the trash, then take the trash out. Even if it is a small thing, or a thing that would take a lot of effort. Let her see you read books about it, look attractive, not needy, look like you will be fine without her...because you really would. Be any girl's dream of a man.