I always thought it was the typical Hemi Tick, but now that you have showed your rod journals being scored I'm a bit concerned.
I did a quick video After I changed my oil.
I've tried various filters and nothing changes. I tried Lucas Synthetic Engine Stabilizer and that seems to barely help.
My truck has 12.3kmi right now. Oil changes were done at 800miles for the intial break in, 2.5kmi and every 2.5kmi thereafter all using Full Synthetic Mobil 1. I use Mobil 1 Synthetic 5w-30. I might try 5w-20 to see if anything changes but I think it'll be a total waste of money because the truck doesnt even get to full operating temp before it starts the knocking sound which is before it gets to that 30weight rating.
My truck has ZERO start-up knock. Cold start-up the truck is Completely quiet. Knock doesnt start until truck begins to warm up. When hot, it's very loud.

I did a video clip walkaround and rev to show it all. At the end, I stand back about 60ft and its still clear as day.
After a fresh oil change this is what my truck sounds like:

http://s217.beta.photobucket.com/use...47f38.mp4.html

 

dirtydog, won't help with the knock but just wondering on the 4th gens I am pretty sure you are supposed to run 5w-20 due to the mds. I have heard running anything else can be bad for the motor. May be different on your 3rd gen but may want to check it out.

 

THAT sounds like a lifter issue. THAT has a problem.

 

Agreed. That's a different noise then mine.

 

** UPDATE FEB 1 **

Picked up the truck today. New short block, new transfer case actuator.

So far, engine sounds good. I'll keep an eye on it.

It's still grinding from the transfer case when reproducing the below video. Anyone know why this is happening?

 

They should have done a S/B when they saw what was wrong. Engineers who told them to repair it. I want to hear a upclose video of cold start and idle like before. Transfer case is not supose to 'pop' out of gear.

 

When looking at the video, it appears you have positive forward pressure from leaning on the gas pedal while stuck at the apron. What happens when you let off the gas pedal completely, will it go into four wheel drive quiet then?

 

After I get stuck on the apron, I let off the gas pedal completely for 3-4 seconds before engaging 4H, then wait 5 seconds for the light to stop blinking. So, there's 10 seconds of NO GAS PEDAL before trying the gas again.

 

It's definitely not normal and doesn't sound too good.

If you do the exact same thing you did, but when you stop put it in neutral, engage 4wd, then engage reverse and then put it in drive would it do the same thing?

 

Yes. I've tried this with Service Manager in the vehicle and it grinded as well.

This is what they think: In the video, when I go to engage 4H, the engagement light should continually flash, and NOT go solid. It should continually flash because since I spun the wheels 10 seconds ago, the driveline is now out of sync. They are now investigating why the light is going solid, instead of continually flashing.

I disagree with this. If no wheels are moving, I should be able to engage 4H. Doesn't matter if I spun the wheels 10 seconds ago. Ugh, this is getting frustrating.