I have a 2011 FX4 with the 5.0L in it - I bought it brand new. I too began to notice this very subtle 'bottom end knock' somewhere around the 7 or 8k mile mark. It only has 12k on it now. I never notice it making any noise when its cold or during a cold start. The only time I ever notice it is after I have been driving it and I slow to a stop and the engine achieves an idle. It will knock very lightly for just a few seconds (15-45) and then it seems to clear up. I'm a mechanic and I have built countless engines over the years - it sounds exactly like a rod bearing that is just starting to get loose...like its just now getting about .001" out of spec.