I didn't see any cracks on the manifold anywhere. Timing is computer controlled, but has no knock sensor (weird IMO).

The part that I don't understand is that #3 knocks ALL the time if I pull it's plug wire or disconnect it's injector. The only way I can get the knock to change is if I loosen the rockers. This is all during idle of course.

Rod bearing on #3 rod. The slightly higher revs/load reveals slop in the tolerance?

That's what I think as well especially after the issue he had with bearings during assembly.

That's what I thought but I plastigauged it with the new bearing and it was within spec.

If you still have the head off rotate the engine by hand and see if you feel anything catching. Also watch the #3 piston to see if rocks or does anything different than the rest.

I did that when I first pulled the head off but I'll do it again. It rotates nice and smooth, which is making me lean towards the valves. I'll pull them out later today when my neighbor gets home from work.

There is no movement with the piston as far as side to side goes. I also turned the crank to get #3 to start its downward stroke and pushed on the piston and it didn't move.

Went back to the listing where I bought the head from and found this:

Details:
Brand new heavy duty stronger casting than factory
All parts are reconditioned factory pieces
Head is assembled with new valve seals
Head is complete and ready to install

Being that the parts are reconditioned, I wonder if they used something that wasn't good.

They check everything so I doubt it. Did you listen with a stethoscope before you took it apart to see if you could pin piont the knock?

I tried to pinpoint it but wasn't able to. I just know it was internal and related to #3.