Is it possible there is a part of the loom that is chafing somewhere causing an intermittent short circuit? I would be taking a very close look at the grommets where the loom passes through the body panels.
For safety, one might even consider a separate switched live feed to the ECU that could be fed through a length of Aeroquip or similar braided hose to ensure that even if you lose power elsewhere, you won't lose the engine.
