you should replace with new ones. the old ones swell and make it hard to get the pump seated back in or you pinch them. new ones are tight on the pump housing and go in easier. part # po121.02A8 HARLY.
I take it you lubed the o-rings with some engine-oil first. The outside "plate" of the fuelpump is not supposed to sit flush with the outside of the frame. It sticks out a few millimeteres. Don't know if this answers your question..