I went through the same thing with my partner. Her previous relationship with her bf of 4 years had been an open one and she'd been seeing other people in addition to him. They broke up and then when we got together became monogamous. But it drove me nuts thinking of her as having all this experience (that's what it was for me), that all these other people had seen her naked, had sex with her, and also that she had so much more experience than me and I've always considered myself as being fairly experienced sexually.
Things don't make sense sometimes. I think you're gonna be okay, honestly. I can't remember at what point this problem stopped mattering to me but it did. It literally just went away overnight, and I don't think I can stress enough how bent out of shape I was about this, and paranoid that I wouldn't be able to come to terms with it, wouldn't be able to get over it and that my inability to do so would end our relationship. But now it's fine. I rarely think about it at all, when I do it's in passing, and the odd time I have a tug of anything similar to what I used to feel it generally goes away in a few minutes.
So. Just keep on with what you're doing. You realize the rationality in this situation. That's the most important thing. Just keep pursuing it and eventually you'll get through it. It might take some time but you'll get through it. Here are the things I had to do:
- be honest about things that bother you. If you're having a really hard time, just tell her, but be up front that they are your feelings and not hers. Sometimes I have to clarify: I'm not mad at you. I'm having feelings about this situation that's happening that I have no control over.
- look at your stuff. Is it abandonment stuff? Is it pride or ego? Is it care and concern? Possessiveness? Underneath every discomfort in life is a wound, and our wounds are usually not pretty to us. I feel like the more willing we are to look at them for what we are the better the chances are that we'll be able to heal them.
- actually do something about your stuff. For example, what you've done by posting this thread is a big step. You want to get through it, and by posting you are admitting that you don't really know how and asking for others' experiences and opinions. If it's something really deep - like abandonment - it might need some extra steps. If it's envy or jealousy, same thing, because those can be killers in relationships, especially if we are unable to acknowledge that they are just feelings and that the other person is not CAUSING US to be jealous or envious.

Just my two cents. Hope everything works out for you guys. Sounds like you've got something worth fighting for.