So I'm curious about the code reader issue. Usually you plug it in and let it detect the protocol then turn the key to the "on" position (not start) and it will connect to the car's computer and read out any stored codes. Is your code reader telling you there are no codes found?

Also (and I know you already replaced the battery) try disconnecting the negative cable on the battery and leave it off for at least 15 minutes (to reset the car's electronics). Then hook the battery back up and try to start the car. Let us know what happens.