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Turbo and exhaust are on for good now. Did a test fit of the manifold to make sure things were falling into place like they should. So far no problems!
Looking great! You might check to make sure the coolant neck is fully seated. Sometimes the bolt circled in yellow needs to be ground down or low-profile (no rhyme or reason for when it works, so far as I can tell). Also, I ended up using a pressure plate bolt (iirc) for the one circuled in black, since it otherwise stuck up too high for the hard pipe.
Yep, housing has been drilled. I have no problems with the upper coolant neck being fully seated, but I will look into using a PP bolt in that black circle. I was looking at that a few days ago and was wondering if it would work. I reference your thread quite a bit!