My problem was someone used a solvent-based motor flush, didn't drop the pan afterwords and the debris it shook loose scored the crank journals and main bearings. Had a crank kit installed (under warranty), new exhaust manifold gaskets and one new manifold (it had cracked), and new head gaskets because the heads had to be milled and the valves ground (the mechanic installing the crank kit didn't compress all of the valve lash adjusters before re-assembling the engine and it bent valves on initial start after the engine was re-installed in the truck). Even after an almost complete rebuild, the engine is still a little noisy. Its noisy because the 5.4s are noisy...my buddy has a 2001 F150 Super Crew and his 5.4 rattles, too. You get them over 75K and most of them make noise. I just turn up the radio and hit the trail...it runs strong, burns no oil and goes all day long without any problems other than being VERY thirsty!
Since the rebuild I'm using Valvoline 5W30 synthetic blend.