Jasper probably still does them. When my 5.4L died (cam chain tensioner seal blew starving the top end) they used a Jasper engine which IMO is a better built engine. They used their own US sources graphite coated pistons and oil pump with a steel backing plate. Apparently the OEM pump had an aluminum backing plate that would flex away at high rpm and dump oil pressure off.
I ran the **** out of that 5.4L, 5 minute full throttle runs up 6% grades with 10k in tow, off-roading, etc. Never an issue.
Wish I would’ve kept it. My engine needs a replacement, same as OP. It won’t be covered due to the Whipple tune unless I can prove defective “XYZ.” Two buddies have these trucks and BOTH have mechanical noise at startup, rough idle from cams being out of sync.
I need a truck though, may be time for a Toy.
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Your story is also the same reason why I wish I kept my Gen 1 and repaired what was needed. It's a shame because I LOVE the Gen 2, styling, creature comforts, performance, etc. Is there any way you can ask Ford to prove how the tune caused a failure when there are guys like me who have completely stock trucks that are experiencing the same issue? I hope everything gets sorted out for you