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Alright, I got me a 99 F250 with the 5.4 about 6 months ago. Ever since I got it, it makes a rattling sound at low rpm and then when I begin to accelerate. However, once it gets up to higher rpm it stops rattling. It doesn't seem to be a problem, but its just one of those annoyances. I have opened the hood and tried to find the noise, its almost sounds like the fan is rubbing, but its not. It has a rattling sound like its metal on metal rubbing. The truck is stock, so has anyone else experienced this? Thanks.
My truck has a noise similar to what you describe. It took a while, but I narrowed it down to the forward drivers side Cat. Something inside the cat is "rattling". I'm not going to mess with it 'til it blows out or fails inspection. It's just annoying.
I have a '99 4.6l that had a rattle as well as a leaking head gasket, passenger side no less. I replaced gasket and also found the timing chain guides were worn to the metal which caused a rattle sound. After replacing there is no noise and a remarkable amount of power gain.