Yep, you got a manifold leak. Remember, I asked to check the manifold by spraying cleaner around the injectors and all around the intake? Thats what we were looking for. A intake leak, coupled with a EFI's ability to adjust itself on the spot within a millisecond, can wreak havok with the motors tuning.
Now, next time you go back together with the intake manifold, leave the manifold end gaskets off, and just run a big thick bead of silicone on the front and rear, with the std. intake manifold gaskets on the manifolds sealing face where it bolts to the heads. I've always had the end gaskets interfer with a good manifold seal, I just toss them in my toolbox, I use them to layout holes or for a pattern if I'm doing custom intake work, after I use them once, I toss them. Just run a big, thick bead of silicone at the ends.
After the motor has run hot like that, I'd, if it were me, pull the heads anyway, and make sure its all as it should be! Correct lined up gaskets on the head decks, make sure all the holes are uncovered, have the heads checked for cracks, have them straight edged, then straight edge the block your self. All you need is a precision machinists ruler and a .002 feeler gauge to check it.
Then, go back together with it. While your doing that, look at all the cooling passages and into the waterjacket, look for rust, obstructions, anything that can impede waterflow.
That way your sure all is as it should be. I don't take chances with motors. If it were me also, its only a 15 minute job, I'd yank that waterpump also, since its a main part of your cooling system, I'd put a new gasket on it also, just to check out the impellar and the bearing.
Just take your time and redo the gaskets and all. Your gonna be a great mechanic!