Ok, I apoligize for the long post, but I am trying to give as much info as possible.

Vehicle: 2003 ML55 (w163) - 84.000 miles

I have a noise, and it sounds a little like a rattle, mixed with a deeper ticking. It seems to be coming from on top of the whole pulley system.

Video 1 with serpentine belt on:
http://www.youtube.com/watch?v=mcE-N...ature=youtu.be

I does not appear that the noise is from the pulleys, but we might have to revisit that.

Video 2, this is the noise with the serpentine belt off:
http://www.youtube.com/watch?v=N4U2V...ature=youtu.be

The rattle is still there, and again it seems to come from the, I believe, is the air pump or the timing chain? Since the pulley are not moving I almost want to rule those out as culprits.... but, let me know.

To even further rule out pulley noise being enhanced upwards, I now hand spin the pulleys to look for obvious fails. In short, I did not find anything really bad, but please have a look at how freely the water pump and tensioner spins. Should they spin THIS freely?

Video 3, this is the water pump pulley spun by hand:
http://www.youtube.com/watch?v=HGomH...ature=youtu.be

The only noise is a little bearing noise, but no wobbling or obvious play or excessive noise.

Video 4, this is the tensioner pulley spun by hand:
http://www.youtube.com/watch?v=lHaTr...ature=youtu.be

Spins like the water pump, very freely, but otherwise fairly quiet and no noticeable movement.

Video 5, this is the idler pulley spun by hand:
http://www.youtube.com/watch?v=tgyfO...ature=youtu.be

I initially replaced this because everyone thought this was the one making the noise, so this is brand new. The old one spun like the water pump and tensioner, but the new one only spins a few rotations. If the water pump and tensioner pulley should both be spinning like this, I might have to repace those too? That wouldn't fix my real concern, which is the noise though, right?

Let me know what I can do from here? The noise truly sounds like it is coming from the air pump, but I have yet to find someone with a similar problem by searching everywhere. Could it perhaps be the timing chain?

 

Sounds to me like you might be right on the Air Pump. Have you tried using say a large/long screw driver or stethoscope (they sell them at auto parts stores) and putting it up to your ear as you touch different areas were the sound might be coming from? Obviously you can't do that to the pullies in the front, but that to my mind is not the issue. But like the Air Pump or the Timing Chain Cover Plate. You will hear the noise real loud and clear when you touch what ever it is that is making the noise.
As you said about the pullies, they should be like the one you replaced. Germans make good bearings, but they don't last forever!