Here's a link about how flanges are supposed to fit.
I found that nipples were always sore with pumping, but olive oil and lanolin helped. I switched to a pumpin' pal angled flange months into my EPing experience, and that also helped with the abrasions underneath my breast. Some moms on here have had bad experiences with them, and they're not perfect, but they worked better for me because I have large nipples (on small breasts), and it just let me get a bigger size.
I did find that the smoother vacuum on Medela's Symphony was a lot easier to deal with.
I just wanted to mention that I read a note on a different thread the other day from a woman whose baby had a five-month nursing strike during her first year, and now she has just turned two and is still nursing. If you keep up the pumping, you never know what will happen!