So it was running essentially fine, then Jeep pulled the front of the engine off, and now it's busted. I think I would share your suspicions. Metal in the fuel? Pull the filter, cut it open and inspect it. What are they even suggesting by metal in the fuel? How is that a suggestion of petrol in the system?
I'd at least access the timing belt and ensure there is tension on it so it couldn't skip a tooth. Then, if it is misaligned there's only the possibility that it was installed incorrectly.
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