This is... really, pretty good! While I may not agree with some of the designs here for their complexity, there's enough depth and decent balance for DMs to use when players want crafting beyond 5e's shallowness. There are a few places where the wording could be tightened up a bit ("When you make a Crafting skill check for brewing" in the Calligraphy section, for instance), though.
What I might suggest to get around the weird "subtract gold from your inventory" bit is to have a resource associated with a tool kit you have, that you can add to by buying them from an appropriate store or collecting appropriate ingredients. So you could say, spend 50 gp to have 50 gp of calligraphy resources, which is a pool you could subtract from when you craft with that tool. This avoids the pains of a more complex, piecemeal crafting system but also avoids the whole "you turned gold into alcohol" thing.
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