I personally modded peat to be burnable into charcoal. Unlimited fuel from lots of collection labor. Requires some rebuild of the inorganic_soil. Sadly, anything you do will require a regen.
Adding anything new to the raws requires a regen of the world. New raw files, new entries in a raw file, and any change to the entity files (such as permitting your new reactions). Modifying an already existing entry in the raws (but not entity_default) is usually compatible and will not require a regen.
There are a few rarely-used reactions that are good candidates for modding an existing game without screwing things up to badly. MAKE_WAX_CRAFTS, MAKE_SOAP_FROM_OIL, and just about any of the redundant smelter reactions (such as PEWTER_TRIFLE_MAKING2, make trifle pewter bars (use bars)). I say pick one of those and make it a fuel producing reaction.
Example:
I will never ever ever use PEWTER_TRIFLE_MAKING2, where you make trifle pewter from bars. If I need trifle pewter for a mandate, I will smelt it from ore. This makes the reaction redundant for me personally. I will change it to produce fuel.
How should I get my fuel? I could cheat and setup a reaction to produce unlimited fuel for no resources, but that is not fun. Instead, what would a good dwarf do? Fuel my metal industry with quarry bush plants.
In the reaction_other.txt raw file, change the entry for PEWTER_TRIFLE_MAKING2 to the following:
[REACTION:PEWTER_TRIFLE_MAKING2]
[NAME:burn quarry bush into charcoal]
[BUILDING:SMELTER:NONE]
[REAGENT:A:1:PLANT:NONE:PLANT_MAT:BUSH_QUARRY:STRUCTURAL]
[PRODUCT:100:1:BAR:NO_SUBTYPE:COAL:CHARCOAL][PRODUCT_DIMENSION:150]
[PRODUCT:100:1:SEEDS:NONE:GET_MATERIAL_FROM_REAGENT:A:SEED]
[PRODUCT:50:1:SEEDS:NONE:GET_MATERIAL_FROM_REAGENT:A:SEED]
[PRODUCT:50:1:SEEDS:NONE:GET_MATERIAL_FROM_REAGENT:A:SEED]
[SKILL:SMELT]
Then build some huge quarry bush farms. As a bonus, you could end up with lots of rock nuts by setting up a fuel industry this way, which means lots of rock nut paste and oil for your dwarves to enjoy.
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Of course, you could also just use your alternative stone concept, just replace an already existing reaction with the new one, but do not change the token of the reaction (the part that says REACTION:"make_blah_blah")