It is very possible that the end stops got fried. Even if the configuration is wrong with regards to whether or not the end stop is inverted, it should still toggle when you press the switch and do a M119. And why does the Z-Min toggle when you press the Y end stop? That suggests you have the wrong board configured or something plugged in the wrong place. That is worth checking out because that is doesn't seem right and resolving that may fix the other end stops.