That will go away I think you're right on the id. They're annoying because the bubbles get chewed up in the powerheads and you think there's a microbubble issue somewhere in the system. When only my T5s are on the bubbles stop being released and my water clears. I'm pretty much clear of this now on my new setup.
Good to hear about the vertical 2x4s. I was more concerned about that then the plywood.
I think the valve thing needs to be sorted out though. You can drill your emergency drain into the back or side panel and add a 90 on the end so it's above your primary.
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