Thanks for the input thus far everyone! I was able to band-aid together some exhaust for the truck, its much quieter now. Here is a new video with exhaust installed that might be more helpful for those who know what to listen for.

http://s824.photobucket.com/user/keenebolter/media/58%20Apache/Video2_zpsa3m21yox.mp4.html

I moved around the engine compartment trying to see if I could find a place were the noise was louder. I think the knock is stronger sounding from the passenger side. I looked around for something obvious loose or hitting but didn't see anything. So maybe the next step is to take off the valve cover or the side lifter cover and see if there is anything not moving or binding there? Thanks for the help!