It takes more voltage to ignite a lean mixture than a richer one, that is why often slight misfires and stumbling can occur at low loads and part throttle but not at higher loads.
OP have you inspected the COP boots closely, for signs of hardening/cracking and/or a "burned" smell? It is not unusual for them to harden up and lose some of their insulative property--when that happens the build up of voltage needed to ionise the plug gap can be slowed and weakened, again affecting ignition of leaner mixtures. Many COPs have been replaced unnecessarily because the boots were bad.
Most FLAPS stock new boots or you can get them online for $3 a pop
The spark knock you are experiencing could be because each manufacturers heat ranges differ, and the NGKs are running hotter than the OEM plugs. There is no standard for spark plug heat range designations and often the cross-reference charts are not entirely correct. I would not use any but Motorcraft or Champion plugs in any n/a 4.6, and only in booted or other power adder builds if there was some specific reason to do so.
The Champion stock # 3401 single platinum (the center electrode) plug that seems to behave well in our cars, or Motorcraft's SP-493, also a single platinum plug. Unlike the coil pack EDIS used on the '96 through '98 GTs there is no need for double platinum (both electrodes being precious metal) plugs in the '99 through '04 V8s as the COPs all fire with conventional polarity.