Sorry to hear about the hassles. I love the look of my sandbed but yeah it can be a hassle at the same time. I'd get a sand-sifting fish to help you out. My sand was also forming solid layers (but fused with what may have been cyano) which quickly disappeared with my goby always sifting.
Interesting idea about the pellets too. Maybe you should suspend their operation until the tank has a decent bioload. Your skimmer definitely looked severely under-worked when I saw it.
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