I'm not sure how to add coal in a way that maintains 'flavor', but you could change the charcoal recipe to produce coal pretty easily. Just change line 78 in StonesToOre.cs from new CraftingElement<CharcoalItem>(1f) to new CraftingElement<CoalItem>(1f).
For crafting, it would be very easy to make it more expensive.
Find the line new CraftingElement<GneissItem>(8) in StonesToOre.cs and change that 8 to something higher.
For mining, it gets a bit more complicated, but it's still possible.
You can open Mining.cs and change the line...
Makes metal ores easier to get by making them part of mining normal stones and by adding crafting recipes.
In the wake of 8.0.0 world generation bugs, this mod restores some ability to have ores. It also works in properly generated worlds, if you just want to make getting ores easier.