Some people hook up a battery charger to sensitive electronics...not a good idea. This type of power has a ton of ripple or AC component associated with it and its hell on the sensitive stuff. A battery has absolutely no AC component and it's great for this application.
If the +12 volts is getting clipped somewhere in the harness then powering it remotely with an external source will let you know. The only other way to do it is unplug a bunch of stuff including the PCM and start testing your power/reference wires for resistance to ground. Do you have a pin-out of the PCM?