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Looking again at the picture of the roots, unfortunately it looks like you've got a case of root rot. See how they are brown and squishy looking. This is from too much water or too much time in the water. I would turn off your bubbles immediately and lower your res level as much as possible. Then I would search about it as much as possible and learn everything you can. Not sure if that would cause the spots on the leaves.
Not 100% sure though since I have never had it. Please someone else chime in here and disagree or agree, so his success doesn't depend solely on my advice.
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