Do you have a check engine light on or any misfire codes stored? Notice any rough idle or misfire momentarily on cold start-up?
You have a plastic upper intake, correct? These are problematic in that directly behind the throttle body there are 2 small coolant passages adjacent to the EGR inlet to the intake. Hot exhaust eventually cracks the plastic to the point that a small amount of coolant can enter the inside of the intake. Not enough to cause any problems at first, but as it progresses, well, I’ve seen them hydrolock.
Sounds like you’ve looked at all the common problems. Maybe it’s time to pull the plenum.