i think that you are using 2 dc-dc regulators, where you could be using just 1--
i can't find any info right away on that p4d03 regulator, but it sounds like that is similar to the m1-- both will regulate the voltage going into the computer.
for now, i would recommend just using the m1 for carpc power.
to hook it up, just tie the 12v, and acc lines together to one of the the 12v outputs of your computer power supply, and connect ground to ground-- this should get the carpc to start up. i believe that there might be some jumper settings that might need to be setup, though, i am not familiar enough with the m1 to know them, so you might need to check the manual for those.