The intake piping and air filter canister look like they should flow pretty well. What would an acceptable pressure (vac) reading be post filter, before compressor inlet?
this I don't know.
I'm drawing from my time with the LLY Duramax engine. the compressor map in stock configuration has the turbo running at the surge limit. this is because of a poorly designed air inlet pre-turbo to post air filter box. By changing out the "turbo mouth piece" or the turbo inlet pipe to the stock LBZ piece, you drop IATs by 75 degrees, go from 22 PSI MAP to 19-20 PSI MAP, increase MPG by 2 MPG, and make more power. With the addition of larger and smoother intake pipes to the air box and cutting holes in to the air box, these advantages become even more pronounced. So If your truck is making these noises, I would assume that there is a restriction there and by doing something like what I described might net you gains like what is experienced with the other engine.
This works because the computer is commanding XXPSI from the turbo. The MAP sensor is telling the computer that its seeing YYPSI. So the computer begins to command more from the turbo until it sees XXPSI from the MAP. In essence, the computer is telling the turbo to put out 20PSI. The MAP is telling the computer its seeing 18PSI at the intake manifold. So the computer begins to force the turbo to put out more boost until the MAP is seeing 20PSI. But, at 20PSI MAP, the turbo is working as hard as it would to make 23-24PSI. The reason for this starts at the turbo mouth piece. Its got a 90 degree bend in it and at that bend and through the bend it pancakes down from a 3 inch round inlet to a 1inch by 2.5 inch rectangle shape back out to a 3 inch round discharge in to the turbo inlet. Moving forward, the intake tube goes from 2 inches to 2.5 inches and the air box has one hole in it that is sealed to the fender and is 3inches by 4.75 inches. By replacing all this with free flowing equipment, you lower the PSI, but allow the turbo to flow more CFM per PSI.