Regardless of the percentage of likeliness of conceiving, people get pregnant everyday! People get pregnant on the pill, shot, with condoms breaking, etc.
It doesn't matter that neither of you had an orgasm or that you "wiped" before reinsertion. Precum can get her pregnant also and that can come out at anytime.
Since her periods haven't been normal anyway then she most likely is just stressed and therefore not getting her period. I suggest that she goes in for her annual exam, and gets on the pill. And you should use condoms even if you are just inserting three times. It only takes one of those little guys to get her pregnant and they come out whether you orgasm or not.
But, just don't stress and try to keep her relaxed also. The pill would even out her periods also.