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I agree with G.
Keeping the tank "Fish-free" for 6 weeks will most likely solve your ich problem as the parasite cannot live without a fish host. 6 weeks without fish should cover the entire life cycle of any form/stage of the ich essentially starving them to death.
If I remember correclty the emperor filters have bio-wheels. This may account for the elevated nitrates (the biowheel can become a nitrate factory over time). A refugium would certainly help with the nitrates.
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