if its a rod knock or wrist pin...do a power balance test...disabling the cylinder should change the noise and pinpoint the bad cylinder

 

Just did an oil change on it because it was due for one (every 3k) and with the new oil in it it still made the knocking noise but did not last as long as before. Maybe 2 mins or so.

Thats what i was thinking also. A rod knock would keep knocking no matter what. Not just for a couple mins then go away. Completely stumped

 

There are procedures to isolate or pin down pretty close just where the knock is originating Shorting out the plug (coil disconnect) and if a rod the knock will disappear
If a heavy rumble knock , possible main brg. Something you should know, If the converter to flywheel bolts are not tight it can produce a noise just like a rod knock. That is easy to verify , just remove the flywheel lower cover and check the mounting bolts.

 

I thought I had a weird bottom end noise also. Would appear as soon as it would warm up. Try turning on your AC and see if it goes away. If it does, it can be AC tensioner related. That's how I figured mine out. Take off both serpentine and AC belts and see if the noise is still there. That will also help you hear it better since there are no accessories creating extra noise.