CARB regulations require the transmission match the engine your are using and not the other way around. Technically the engine you purchased would be a normal "engine swap" if the transmission you were installing was a manual.
The question is will the referee allow you to modify the new engine by removing its AIR injection system. If no other emission component is effected by the removal of the AIR (i.e. downstream injection ports, CAT ports) and all other engine sensors and functionality is identical to non-AIR installed engine, the referee might allow the vehicle to pass by not declaring the AIR removal a "tamper".
See if you can get a hold of an actual referee on the phone. They might be able to give you info specific to you. (800) 622-7733.