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The respective goddess cube you need to activate is the one on the slide in Eldin, when you're finding the key pieces, aim for the geyser after the first tunnel. The actual chest is on a small island NE of Skyloft, got to have the bird drop you off then climb vines down to get it.
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The cube that unlocks the Treasure Medal is located on a small slope on the right/behind the Bokoblin village next to the temple entrance, before you cross the bridge made from the collapsed tower. The chest location previously mentioned is correct, however.