Right i forgot about that yeah they have 2 pins now that you mention it.I think the UD2ATP has a switch on it to do 2 different type of set ups one for capcom style button set up and one for neo geo style set up. I don't know if that will help you at all though.
I don't, there is no way to connect the kick harness its just an expansion I/O Cart port and another expansion port and some VGA port and a CN3 with 10 pins.How are you plugging in your kick harness from the ATP? If you aren't, you'll need something like a JNX Atlas to plug in the kick harness to, as Atomiswave uses buttons 1-5 from the JAMMA harness.