I finally got the chance to really look at the flex plate and there was nothing wrong with it at all, I even started it with the cover off and heard nothing... it has now gotten loud enough that you can hear it when you open the hood...
I drained the oil the other day into a clear tub and saw no metal shavings or anything...
it's not the U joint because it makes the noise in park or any gear. Im thinking it could be a rod or something to that effect... any ideas?
Also, I bought this engine Feb. 15 of this year and started hearing the noise less than a week after installing it, so if it is the engine would I be able to get a refund on warranty from the salvage yard, I noticed the noise before the warranty was up but just didnt know what it was.

 

I listened to the video as well and the only that hasnt been mentioned is that it could be a bad PCV valve that is rattling like crazy or an accelerator cable resting on the PCV hose. Those are my guesses. You can view this by looking to make sure nothing is touching the PCV hose, also if you touch the PCV valve while the engine is running it should not be vibrating constantly, mine has been doing this since I replaced it so I am going to replace it again (after having taken one back to the store already). Good luck getting your problem fixed.