I'm definitely not an expert, but stop going back to her every time she she comes calling. Tell her you don't know if you are interested in this R anymore and that you cannot live with her seeing OM. I couldn't tell from your posts if she has issues with you or not, but if so, accept them, validate her concerns and work to be a better man. If she wants to reconcile, tell her it will take some time and you need to set boundaries and have a transparency plan (thanks puppy). You are not willing to be 2nd best and there can be no more trips to Boston.
I probably am not the best at this, since I am still a newcomer with my own problems, but you have to stand-up for yourself man. Do not let her walk all over you like this. I am in my own situation with at least an EA and possibly a PA after 23 years together. It has been 6 months we have not been right and it is breaking my heart, but at some point, enough is enough.
I recently told her that if she is not willing to work on the R, then there is nothing else I can do but give her the D she has filed for. It is not what I want, but it is what I have to live with. Tell her if she wants to continue with OM, you will be done with this R and filing for D. I know that is harder than anything you have ever done in your life, but it is the only way out. How long has this been going on? It is time to do what is best for you and the answer is not always obvious. It is time to live life for yourself and for your son. Focus on that relationship and be the best man that you can.
Maybe puppy or DDay can help you more. I am still a rookie and hesitant to give too much advice.