First, let me say that you are doing things correctly.
You know this is a process and you're treating it as such. It will take time, lots of it, and you're aware of that.
You're also aware that there won't be a straight line of improvement either, there will be stops and starts, some days and weeks will be steps backwards.
Therapy and counseling are involved and that's wonderful.
You also know and are circling back to the same things many times and that's good to do, to see if her responses change, if her thinking changes etc.
You also know that many of her "reasons" aren't valid, that they were just surface deep or skin deep and you've kept that in mind as you are going forward.
Real issues that aren't just surface deep won't and can't be easily swatted away. When both of you dig into them, they'll remain and you'll both know those are real issues to address and deal with.
You also know there are issues outside of her affair to be worked on and you wife certainly knows this now.
She's come to the realization that she is messed up in many different ways and that she has been for so long. Choosing to carry resentments, for some minor things in many instances, for such a long time, for choosing NOT to communicate with you, for putting walls up in and out of your bedroom and of course she's deal with the weight of her incredibly hurtful decision to choose to have an affair, to say nothing of her choosing to badmouth you for so long to so many, including family.
Obviously I don't pretend to know your wife so my next comment is just in general, not specific to your wife.
Some waywards want to change and improve and they begin working hard on it, going all in. Some of those same waywards finally begin to grasp and see how badly they behaved before and during the affair and not just regarding affair things either and it overwhelms them. Some of those waywards use that to fuel them and to continue working on themselves and their marriage.
Other waywards lose hope, say it's impossible, that it's too much to overcome, it's not worth it, it isn't going to work out anyway and they give up and choose to divorce their betrayed partner.
I'm not saying this happens quickly. I suppose it does sometimes, but usually when this happens, it's later on, a year later or two years down the road.
They try so hard, then they hit bumps in the road, they trigger, their spouse triggers, they bump into the AP unexpectedly, like say at a grocery store or a gas station and they go from feeling good about things to triggering and an argument ensues.
Some waywards throw their hands up and say uncle.
Earlier you said you felt as if your life with her has been a lie and you were referencing all of it due to the way she was.
I hope your wife has the intestinal fortitude to withstand a LONG and BUMPY road of years and years without giving up hope and thinking it's hopeless and useless for her to continue trying.
I hope she has the intestinal fortitude to accept that she's made mistakes and remain committed to working on them and correcting things about herself when she's faced with having to deal with this about herself day after day, week after week month after month and then for a year and then even longer.
It overwhelms many, sadly. On the other hand, some are able to dig deep and withstand the long term "pain" and suffering that they will have to endure and they willingly choose to hit it head on and to use that to fuel them to continue forward on their path of change and improvement.
I also hope that when your wife is much further down this road, that she doesn't say to herself that she's a much different person now than she was before and she wants to go her own way now that she realizes who and what she really is.
Some waywards do that, they say they chose their partner years before, when they were younger and "broken" and now that they're older, wiser and no longer "broken" they know they shouldn't have chosen their partner.
Two people who are really committed to each other know these things and choose to continue on as a team, as partners, working together. They realize that all of us, change as the decades go by. None of us are the same people we were when we were young and met someone. We're not the same in our 30's, after children as we were when we met each other in high school or in college.
We're not the same in our 50's either and on and on.
Some embrace this, others run from it.
My hope is that both of you will be able to withstand all that is still in front of you both regarding all of this and embrace it, together.
Sadly, that's not known as of yet.
So many things in life are "to be continued."
Last point. There aren't any shortcuts, nothing may be skipped or rushed and hurried through, but you know that. I hope your wife knows that and really understands it too.
Good luck Doc and take care.