With liverock, 1 to 1.5 inches of sand is perfect. Any more is actually not ideal, in fact, so you've luckily stopped right where you should have. All the action occurs in the top inch or so, and deeper than that things get very inefficient.
Turkey baster. You'll have to work on smaller areas at a time, but a turkey baster should solve your sediment problem quite nicely. Turkey basters are also very handy things for a reefkeeper to have anyway, so go ahead and get one.
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