You could "harvest" (bad pun) code from Brewhouse to use during the initial phase, where the player is actually doing the planting. Also the ability to sheer sheep in that mod is cool, and could be implemented in yours.
Of course, you need to get permission.
Marble wouldn't be made from refined rock, marble is a kind of rock, it could be just mined, cut and polished.
As to what the place stone is cut to shape and size specifications, as well as polished if it's for something that needs to be polished, is a masonry.
And to go from Ore to ingots, the player could do. The exact process varies from metal to metal, of course, but all are generally the same. Basically, you put the ore into a crucible, often along with a mix of other things, then you heat it up. Really hot. When the ore has turned to a liquid, you use special tongs to remove the crucible from the fire, and pour the metal into molds.
The crucible is heated within an oven made from special bricks (firebrick). The oven should fully enclose the fire, with only a small hole at the top, bricks are slid over the hole used to put in/take out the crucible. The fire needs to be VERY hot, so it needs to be blown by a bellows.
I have personally melted aluminum scraps in a crucible, with my dad. But instead of using wood, we used propane. I wish I could show you pictures, so you could get a good idea what I'm talking about, but my email won't let me attach files for some reason, and my dial-up has issues with sites like photobucket.
Suggestions on further use of wood, stones and metal are welcome. Ships, weapons, armors and tools have already been suggested.
Shipbuilding requires some stone, it's placed into the bottom of the hull, so as to sink the ship into the water further and provide stability.
Perhaps (would require someone willing to make a whole new tileset of stuff) wood and metal could be used to expand your city and castle UP. You could make a multi-level city, with the original city just lurking on the bottom. But with this type of city, crime rates would soar, as there's a confusing multi-level maze for criminals to hide in, and guards aren't able to cover the whole thing.
OR, metal and wood could be used to move the city out over the water, sitting everything on a series of piers. This would free up more land for farming and such, in addition to making it EXTREMELY convenient for ships to pull right into the middle of town, and offload their goods even closer to where they need to go.