Dealing with ongoing affair -which may now be over

[PeterV2]

So I gave her the apology letter today and she read it and thanked me for it. However she went on to ask why it was ok for my ex to be living with a new man but it was not ok for me. Again I repeated that that had nothing to do with it. I just didn't want my ex nosing into my new life.
My W said there were lost of other incidents where she felt like she wasn't the most important person to me. That my ex trumped her. But this of course was not the case. However that is her perception, or was her perception. I reiterated that she was and is the most important person in my life. She says, "yeah now I am. But for years I wasn't".
I'm perplexed. She's always been the love of my life since we first kissed. My numero uno. But obviously I did things to undermine that and caused her to have the perception that she wasn't #1. Perhaps I didn't communicate my feelings accurately. Perhaps some of my activities and actions caused her to perceive that I didn't think of her as #1.
How can I counter that?

I spent the rest of the day working with her at the RH. At one point she started a friendly playful pushing match - I responded with a push back, a hug & a wet kiss on the ear then continued on with my work. She cooked us lunch and we ate together. She later went to have a nap. So I finished work and came home.

I hope she reads the apology letter again. Maybe I should ask her if she's ready to start the reconciliation process. But I think I'll wait a couple of days to give her a chance to reread the letter and process the info from our discussion.