Yeah, AT uses a different ECU than manual. You can convert a P28 ecu to manual, look into if the same can be done with your P06
http://www.civic-eg.com/viewtopic.php?t=963
Also, I believe your compression ratio will be a little on the low side, using a z6 head on y7 bottom end, since OBD1 D series heads have a larger combustion chamber than OBD2 heads.