You have got to concentrate on the positive things. She pees where she is suppose to. That's great! Pee is so much harder to clean than the poop too.
Joey always picked out of the way spots to do his business too. You can just pick up the poop and put it on a pee pad. I actually kept two pee pads out for Joey, one I put in an out of the way spot, was for poop. I first would put his poop on the pad, than after about an hour I would flush it. I don’t' know if Joey had difficulty pooping at first because he would always do a little jump afterwards and even when he started on the pad, it ended up "next" to the pad. I don't know if the sprays help that much, I thought they were just for urine training.
Maybe someone else has advise on the social problem. I think the more they are around other dogs the better they are able to handle it. She may be just being protective of you.