I have a 3V 5.4L (same heads as your 4.6's), and at about 44K I developed a constant tick that would not go away. I had read the TSB about the cam phasers and other various valvetrain issues, so I took it into the dealership to see what they thought.
"Bah, that's just loud fuel injectors! Nothing to worry about, every 3V motor make that noise!"
At 48K, I got a misfire CEL. I thought it was something to do with the COP's or even the craptastic 2 piece spark plugs, so I took it back into the same dealership. The did their full inspection, and found my # 2 cylinder was dead
After being told it would cost 8-9 grand for a new longblock installed, I paid them for their inspection and took the truck home.
I pulled the passenger side valve cover to see that one of the intake valves was totally missing, along with it's FF and HLA and that valve's cam lobe is knarrled up pretty bad. The only thing that was inplace, was the dang spring. There isn't even a valve stem sticking out or anything.
This was after a lifetime of Royal Purple or Mobile One and the "correct" motorcraft filters, every 3-4K.