Also, pulling the Relay Control Modules out and resoldering all of the relay pins, etc. would be a VERY good idea. The "engine control relay" feed to the PTCM may be the cause here. That relay powers part of the PTCM and all contacts on the RCB are known to go bad in time.

There is a thread here on the RCB fix. The RCB (and other modules) are in the black box next to the battery. The RCB is the one closest to the center of the car, it unplugs easily. You can take it to any radio / tv shop and have them resolder every point on the board for $10 to $30.

I think you have intermittent power to the PTCM. I'd almost bet money on it. That, or the battery is getting flaky.