Help Me Identify This Knocking Noise

Greetings,

I just recently purchased a 2004 Tacoma 4x4 2.7L w/ Auto ~ 95k miles. Now that the mornings are starting to cool down, I have noticed for the second time now a distinct knocking sound.

- Start Truck
- At Idle, sounds great - No Knocking
- After about 1 minute - put in "D" - Knocking begins
- Put it in "N" - Knocking goes away
- Put back in "D" - Knocking starts again
- In "D" - Knocking is consistent at first, but then begins to "cut-out" and eventually after about 30-45 seconds disappears

I never noticed this before on warmer mornings (around 50 degrees F), but the mornings are starting to get down into the 30 range. About 2 weeks ago, I had Toyota replace my tranny pan (drain plug stripped), flush w/ Toyota Type IV, drive belts replaced, battery replaced, and water pump replaced. The fluid was blackish in color before they flushed. Does anyone know what this could be coming from? I haven't been able to pinpoint the noise yet since I cannot let off the brake as it only does in when the transmission is engaged (i.e. D or R).

Thanks.

 

I was able to finally get a recording of the knocking noise. The audio file starts with the phone underneath the vehicle. Then about half way through I popped the hood and put the phone near the valve cover. That is when the knocking noise seem to intensify and eventually disappear. It sounded like it was coming from the engine but I cannot be certain.

Note: I started up the truck, and put it in D about 5 seconds later. Engaged the parking brake and began recording.

https://soundcloud.com/yotanut/toyota-knocking