Ran it without the belts, noise still there.

I have to admit I am getting pretty frustrated with this noise. It's a really loud rattling/ticking noise like loud valves but x10 as loud. It started at the beginning of the summer and this is what I have done thus far with no luck:
-Replaced timing chain
-pulled each plug wire to try to isolate independent piston/bearing noise... found nothing
-took it to toyota for my steering rod recall and had them spend an hour going over the engine looking for the noise. They found nothing and said "it's internal" and they would have to dig into it to find the noise
-Started taking the whole engine apart hoping to find something eventually... this grew into and entire rebuild (even though the engine is only 2 years old). The machinist wasn't able to find anything horribly wrong with the piston/crankshaft assembly, only said the bearings were wearing poorly for such a new engine. They polished the crank, checked tolerances on the rods, and the block needed decking. They also looked over the head while I had it resurfaced.
-Sent injectors out to be rebuilt
-Put engine together while carefully checking every moving part for a possible cause of this noise.

After all this I got everything back together and the same noise persists!! I just got done removing the belts to double check the possibility of the pulleys making noise. Anyone have any other possible ideas on what I could try?? I've combed over the entire engine with a stethoscope hoping to find a source, but nothing really stands out. From the naked ear it sounds like it is coming from the intake plenum area... Thanks for any help... this thing is driving me crazy!

Dan