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Stacks of crystals sell more often then single crystals, so they would be a better option when calculating costs. But then there are some items that have stacks that sell once in a blue moon, and the price is still taken from that stack.

My suggestion to fix this is to simply take the price of the item that sells more, single or stack. Whichever sells more, will be the best basis from gathering info from. That would fix this problem.