The 99-03 4.6L engine doesn't have cam phasers (which are known for knocking noises). It's a pretty basic timing chain setup in your engine, with two chains, guides, good cast iron tensioners, solid cam gears (no phasers), and rocker arms (roller followers, actually). These are not known for having major issues, but they can on occasion break a plastic tensioner. Especially if correct semi-synthetic oil or regular oil changes aren't done. When a chain tensioner breaks, there's a lot of metallic knocking noises coming from the middle of the timing cover.

If you have a digital storage oscilloscope, you could take a cam/crank waveform and see if it has any timing chain problems. Without that, you might be able to remove the valve covers or even just the cam sensor, and look into the timing cover with a boroscope (small camera) to see if you can identify the problem. Without either of those, you're down to pulling the valve covers off and having a look.