Well, it sounds like despite everything that has transpired you want to be with wife.
Here are the problems that prevent us from moving forward:
1. I still have feelings for the secondary and they are not fading fast enough to help my wife and I move forward and rebuild trust;
Could you please clarify? Fading fast enough for whom?
How do your feelings for the secondary and grieving the break up loss of that hold YOU back from building trust with the wife?
How do your feelings for the secondary and your grieving the break up loss hold WIFE back from building trust with you?
2. My wife sees that everything the secondary did was manipulative, while I see her actions as those of a mono person (introduced to poly by me) who stumbled her way through our connection and opening up her marriage simultaneously.
You don't have to agree with wife. Secondary is GONE now. But if your goal is to be with wife... could figure out whatever her reasonable need is here and if you could reasonably meet it. Then maybe she can LET THIS GO already? Say you DID agree that the secondary was manipulative for a minute... What NEED would hearing that from you serve in the wife?
She needs empathy from you? Needing reassure? Need for primacy? Something else? Is what she asks of you not realistic or reasonable?
You could say to wife "Yes. I see that everything the secondary did was manipulative for you. Remember, secondary is GONE now. How can I provide you with reassure at this point in time? I am HERE. I am sorry this is hard and crazy. I am here with you through this. What needs can I meet for you?"
What about your needs? Does wife understand what your needs are here -- to be able to let go of the ex in a way you can live with? The need to grieve loss without extra grief piled on top? Maybe you need a counselor or trusted friend to help you with THAT portion of it. Because on that one? Wife is not "the guy" to help you process? It just feeds crazy?
See if sorting out the NEEDS for each of you and "who's the guy" for helping to process it helps move it over the hump. You may not be "the guy" for all her things and she might not be "the guy" to help sort all her things. Too close to the issue to be helpful. YKWIM? Maybe if you can each understand each other's need in this you could get closer to resolution?
It sounds rough over there. I am sorry.