Michael, I think you touched on an important point.
"It seems that if your goal is to flip they will just come down on you with code violations and fines until you get sick of them and give up. "
The problem seems to be that there is a hysteria in that area. They want to use flippers as scapegoats when they can actually help the area by bringing up homes prices (if they are successful flippers).
I think it is a situation where people are so influenced by propaganda ,even at the highest levels of local government ( Mayor,etc) that they behave in an irrational way.
Have you considered other local markets where the cities might be possibly be less hostile towards investors... Niagara Falls or Rochester? I don't really know the current situation in these areas but I don't remember my family member saying that they had as many problems there.