With everything he has replaced, I am not sure there is much left that a "heatsoak" would cause errors with. The one exception would be a vaporlock in the fuel rail, and I cant remember if the 2005 models were return, or returnless fuel systems. I know there was a change right in those model years.
If he had a older truck, than I would suggest fuel injectors since the older trucks run in batch fire.. or the older ignition modules (like previously mentioned). But neither of these are relavant here..
Unless the ECM has a crack in the board, and heat soak is causing it to spread apart.. But even thats a stretch.