I recently like last week researched this issue. My lightning 5.4 motor was replaced with a FQR longblock. I was concerned that it would be a Fred Jones rebuild. Fred Jones no longer remans motors for Ford. AER of Carollton Texas is where they come from. Ford supposedly bought this company and oversees quality control. My lightning had a factory long block that was sent to the FQR supplier and retagged as remanned. It was new. I was told that if you replace a motor under warranty for the first year it is supposed to be a Factory line engine. June 1 begins the new model year. If the oil filter that comes with a long block is grey or has a small , say an 1/8 inch yellow square on it then it is said to be an indication of it being a retagged long block that was a Factory line motor. The tags are on the passenger side of the block. Mine came in a wood crate with a cardboard box over it. Most remanned motors come in a plastic two piece shipping container. They may still have Fred Jones on the container.
The facts are still unclear...however.