Latest updates:
Brought the car to my local Ford dealer to have them evaluate it. Same as me, they were unable to identify what specifically was causing the noise. They think it could be piston slap, a wrist pin or a bearing. Their feedback was just drive it, it could last another 50k miles or more despite the noise. They tried shutting down cylinders and noted, as did I when I did the same test, that there was no change in the engine noise. To me this is a key fact! Piston slap, a wrist pin or a bearing should all change sound when the cylinder is de-activated. I asked them if it could be the water pump. The feedback was they didn't think so because they believe that the pump would be leaking coolant badly if the bearing was starting to fail allowing the impeller to hit the block.
Now, having said all that, I still think it could potentially be the water pump. My recollection is that the area of the block that the pump fits into is fairly small. The pump impeller, to work properly, has to have a tight tolerance with the surrounding enclosure in the block to allow the pump to actually work and move coolant. Also, a bearing failure can occur in different ways, for example maybe there is movement in the z-axis along the impeller shaft allowing the impeller to hit the metal directly in front of it and not necessarily the metal around it . . . One other interesting note, for the first time since I've had the rebuilt engine installed, I heard the famous "startup rattle" yesterday. I think this could be further evidence of a water pump bearing starting to fail.
I've also thought this through and there are three additional scenarios that could potentially be causing the noise: 1) An oil pump problem, 2) a cracked piston skirt where part of the piston actually broke off and dropped into the oil pan or 3) a cracked/damaged timing guide knocking around inside the timing chain cover. As part of my diagnostics, I did an oil change to see if there would be any change in the engine noise and there was not. However, I did run the oil from that most recent oil change through a fine mesh screen (one used for straining automotive spray paint) to see if there were any noticeable metal or plastic bits in the oil, and there were none.
I'm open to recommendations on this, but I think my next step is to pull the front valve cover and see if there is noticeable play in the timing chain coming up from the water pump and to the bank 2 camshaft actuator.