If its in time then something has to be on top of a piston or maybe a rod got bent and the piston skirt is hitting a crank counterweight. I know it's too late but there are repair kits for the stripped spark plug holes that don't require removing the head. Cal-van makes a very good kit and I have installed maybe 20 and have not had one come back.
Ford senior master tech
Every 5.4 3V owner should have Lisle tool #65600
8L3Z-6M280-B updated VCT solenoids for 5.4 3V rattle