Hah, I'm an idiot. I posted this in my build thread completely forgetting that I had started a whole other thread just for this problem. The more educated I get, the stupider I become.
I finally had the time to take my skimmer apart last night, and I found at least part of the problem:
That long hairline crack down the intake of the pump is why there's bubbles escaping under the body of the skimmer chamber, and I bet it's got something to do with the noise.
I e-mailed the Canadian distributor for Deltec and Deltec Spare Parts USA last night and they both got back to me this morning. There should be a new intake manifold on it's way to me right now, and they will trouble shoot the rest of it with me if that doesn't solve the problem.