My question is how does me "letting" an affair continue, all the while "working on myself" and staying calm and rationale help my wife understand what she's doing to me every time she's with him?
You're thinking your W is considering your feelings, but she's pushed that aside so as to consider her own and only her own foremost. "What she's doing to you" is in truth what you're doing to yourself as a reaction to her actions, she's not in an affair in order to do something to you, but for what she's getting out of it.
She's going to do what she wants to do, feels she needs to do. You have no control over the affair continuing or not. Affairs can fizzle out of their own accord, so in the interim, you doing your part to make yourself the better option is not a bad way to go. Remember that the breakdown in your relationship didn't happen because of the affair, the affair came later. The A is just a symptom of things gone wrong, and reflects on her inability to maturely work on your relationship at this time.
she's had years to build up a tolerance for hurting me because I have not been what I needed to be and I am to expect that left to her own devices, she'll just snap to her senses and realize the pain she's causing, break off what seems to be a very fulfilling affair, and come back ready to work on us?
She had time, not really for building up a tolerance for hurting you, but for building a wall behind which she wouldn't be hurt by you any more. It's that wall that blocks her from bearing the damage that she's doing to those around her. So, no, there is no "snapping to her senses", it will take time for that wall to come down, just as it took time for it to be built brick by brick.
You have to stop seeing this as something being done against you, and see it for what it is, something which is all about for her. From what I get in your Newcomer's thread, your sitch is relatively young, she's emotionally divorced from you, and most probably in a PA with the OP, yet she seems that she can't let go of you entirely. She's either looking to get out of your relationship and have you make the break for her, or she's giving you a wake up call (but I think it leans to the former as she's feeding you lines to have you make a decision to let her go, and is making moves to be with the OM freely without your interference), so she revealed the affair to you. I also think that her telling you "not to worry" is probably linked to your reactions around her and that's her way of placating you and holding you off until things are in place for her to exit, rather than on any basis in fact.
The best thing you can do right now, IMO, is stop personalizing her actions, don't put faith in her words, start pursuing your own interests and fill up your time with that, letting her go (emotionally) to do what she feels she needs to do, because as hard as that may be for you, and as much as that's not what you want to have happen right now, what you do desire to have happen isn't likely going to happen, and doing the above is more likely to create some void between you that she may be more prone to fill, rather than build the wall.
