Maybe an interim step where you turn the stone into 5x of something (cinnabar tablet?), which is then used in the reactions to produce the metal/crystal? Perhaps produced at a masonry or jewelcrafting, using alchemy skill (the shops have the tools needed to create the tablets, the skill is the knowledge to make them without much waste), or it could just be added to one of the alchemy workshops.
Personally, I find it odd at the lack of interim materials used in DF. It doesn't make sense to me that dwarves only ever work in huge boulders or a whole tree-as-log. If I were so inclined I'd create reactions for "blanks" of stone (wood would make planks), which can then be used in the same way we use boulders now. The number of blanks used for furniture or other items would vary, similar to how materials worked in 40d (though not quite the same; a door might take 2, a statue 10, where each boulder/plank produces 3 blanks). Furniture and other things could still use a single boulder, but they'd be "rough" and have a lower value than items made from blanks. Blocks would be removed; the blanks could be used as blocks are now. Metal would only ever have bars, used pretty much as they are now (maybe increasing the number of bars you get from a boulder, and increasing the number of bars needed to make items equivalently). Glass especially would benefit from this process: you'd make glass blanks, which you'd then either cut into glass gems or mold into furniture. You wouldn't buy sand anymore, but instead glass blanks that you can use as you'd like, instead of having only sand and raw/cut glass gems.
But that is way outside the scope of your mod. Sorry for my tangent. :-p
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