Everybody has a past, but the real issue here is that you have not felt this deep connection to her since the beginning. Research shows that in relationships it is possible to cultivate loving feelings. It sounds to me like for a couple of years the relationship has been loving and trusting, and there’s been no indication of infidelity. These are good things.
If you want to stay with her, start focusing on all of her good traits — in the now. This emphasis on being able to appreciate her and the two of you sharing your mutual love, appreciation and vulnerability with each other can be the way to move forward.
In other words, I am saying talk to her about how you feel. That is how intimacy grows. By being vulnerable with her and sharing your feelings, while not blaming her, the two of you may be able to soar above the past.