2005 Ford F-150 Rebuild or Remanufactured Engine

I had a timing fuel issue with my 5.4 L 2005 F 150 Supercab FX4. Rough Idle/drive. Hard Start. Fuel actually dumping out the exhaust. Friend replace Syncronizers (through the valve cover) Module back by the fuel tank, and a coil. Also changed the plugs. Problem is the same, he also noted that there was considerable sludge on the rockers. I believe he knocked a bunch of stuff into the engine, because the oil pressure will now drop after running for a while. Considering a NAPA Remanufatured engine. Garage will install for $5300. But he said that he will need to do any warranty work. I need help. That's a lot of money.
Thanks! Al