I have had same subtle knock. Mine mostly went away with M1 Mobil Turbo Diesel Truck 5w-40 (Walmart) and a standard size Wix filter. My '04 manual recommends 5w-40 for all temps and xw-30 to 85F. The 30W oils typically have friction modifiers that may prevent the lifters from getting spun by the cam, so they don't fill or wear uniformly. Sites like
www.rpiv8.com think using anything thinner than 20w-50 is sacrilege.
Cam knock was a problem with the 3.9s, and I think the 4.6s have some of it as well, despite the design change to hold the cam in place better.
Checking for exhaust leaks, better fuel, new plugs and wires, all good.