I am not privy to the inner workings of the PCM, sadly, a tuner can better answer your questions. Shoot a PM or eMail to Brad/AJPturbo, maybe Matt @ Gearhead/mattr66. Engines and transmissions are tightly integrated these days, so when you do an engine swap i.e. put in an engine that does not come with that transmission from factory, you have to know what the performance parameters of the transmission are, in addition to the engine performance parameters, to make the new combination work successfully. Someone who is familiar with both the engine and the transmission should be able to rig something up.
circuitboardmedics.com can source and program a PCM for you, assuming it is OEM, give them a call and see what the possibilities are. They would be loading an OEM configuration onto a PCM and sending it to you. They are not custom programmers. The engine would fire, but it would take a custom programmer to integrate the engine and transmission logic.