I have a 99 with the 5.4 and it has this strange fluttering like sound on a cold start and after its been sitting for just a few minutes on restart. It goes away however after driving it for about 1/8-1/4 of a mile or so and it doesn't do it at idle. Just a small rev will make it do it though. It comes from the passenger side/bottom of the engine. Its not a knock or anything. Its gotten a little worse here lately and its starting to concern me. Does anyone know what it could be? Manifold leak? Piston slap?

 

It's going to be tough to diagnose any kind of noise without hearing it. Can post a video? Then maybe we can help more.