I've narrowed it down to prety much under the truck. I think it might be the tranny. It seems to do it until the tranny is warmed up and not just the engine, and it does it when I lightly let the clutch out and give it light throttle, like a slow take off. The sound is more like a rattle/knock, and it only does it right when the engine rpms go up a little it starts at about 1100rpm and at about 1200rpm the sound is gone. It only does it when I give it just barely any throttle. I checked the engine hoist mounts and they are secure, and it doesn't seem to be a exhaust leak since it only does it at a certain rpm with light throttle.

Im going to call my dealer and take it in on my next day off. Any other thoughts of what it might be?

2006 F150, 4.2, 5 speed manual, 14,000 miles.