Thank you for the responses (and the bump, SI Staff).
I can see how perhaps she doesn't want to give the verbal gratitude because she's afraid of it triggering something. I've never told her specifically to say thanks, mostly because I thought it'd be weird to do so. Unfortunately, when we first got married, she turned into someone who would seek first to be offended by anything someone says or does to her. In other words, she looks for the bad in what others do, and she assumes it's directed at her (or something that she holds dear). This attitude has held me back in a lot of ways, because I didn't want to sit through a couple of days of silent treatment and lack of any affection (yes, even after d-day).
The times when I have felt safe to let her know what would be helpful to me, I have been very direct. She turned off her physical and verbal affection soon after we married, and after d-day, I let her know how much those things mean to me. She would be good for a day or two, then back to the same old habits. It makes me feel stupid because I still want to show her affection, my love language, but she doesn't seem to want to return the affection. It's funny, because when we were dating, she made a point to tell me that physical affection was one of her love languages!
An important piece of information (in my profile): Our daughter was born a few months before the first confrontation. It was a rough pregnancy, and we weren't able to have sex after about five months into the pregnancy. It was then a rough delivery, and we weren't able to have sex for a while after that. So at the time of d-day, we hadn't had sex in probably nine months. At this time, she was beginning to heal and was ready to reenter the sexual arena. We talked about it, and how it would probably help me to heal (this was within the first few weeks after d-day, when she was acting a lot more contrite and receptive). Whenever I would bring the topic up after that, or even try to get more physical with her, she would just shrink away, go limp, and turn cold as stone, usually giving some excuse. This was since about last May. It wasn't until December when I finally had the guts to ask her what the heck was going on. She said, "How can I have sex with you and get that close with you if I'm not comfortable with you and don't trust you? It seems like you're always judging me and haven't forgiven me." OK, airtight logic. Right. I was flabbergasted, feeling like I was the one who had cheated and couldn't be trusted. On the other hand, I think her saying it out loud helped her to realize just how ridiculous it sounded, and we finally began to try to return to somewhat normal bedroom behavior.
I guess what I can sum up in all of this is that for 6 months, all she did on her side of reconciliation was to say she was sorry. I asked her immediately to break all contact, find a new job (her boss is the OP, but they do work 3000 miles apart, sometimes she sees him when she travels, though), get rid of any related pics, emails, notes, etc. She did none. And she never kept me up to date on job search or progress in removing said materials. So when I asked her about it last August, she started crying, complaining about how she doesn't have time. This coming from the woman who sits on the couch on the weekend, watching reruns of Downton Abbey and surfing Facebook for hours (or taking a nap). Not very proactive. Basically, taking the "If he doesn't know about it, then it won't hurt him approach", kind of like the A.
That's when I finally started going to IC, because I thought I might do damage to myself. The gaslighting was making me crazy. It was right be I started IC that I found pictures of her and her ex-fiance (not the OP) on her computer in various sexual positions. I thought I would die. I had discovered at the beginning some naked pics of this guy on her computer before d-day, but nothing with her in it. I had asked her then to get rid of them, and I assumed she had. I was just checking on the truthfulness of her progress when I found these. I almost had a heart attack. To be honest, I am amazed I still wanted to have anything sexual to do with her, because now I didn't even have to imagine her with another guy. So wrong and disgusting. I deleted them immediately, but it has taken her until just recently to finally get rid of most of the pics and emails relating to the OP. One year.
Sorry to ramble, but there is obviously a lot of related back story to every one of our situations. One last thing is that she has still continued to lie to me, and when I catch her in it, she just denies and denies until she realizes I have proof, then finally admits it. For example, I found out she was still in friendly, non-business related conversation with OP, something that I was clear was off-limits. I asked her if she told him no-contact besides business, and she says she did. But yet I find out they continued. After this happened a couple of times, she finally admits she said nothing. Basically, she doesn't want drama at work, so she hasn't mentioned it. (Another thing, she didn't actually start her job hunt until about 6 months after d-day.) Yet, she got angry with me, saying the conversations (text and email) weren't anything sexual or anything, and she hasn't done anything wrong. Of course, continuing to lie to me about it is very wrong. Lies were what got us into this in the first place. It just puts us back to square one in the trust department.
IC has helped for me. I'm still trying to get her into IC first before MC together, because she has some issues to deal with in herself before an MC will do any good.