What I've done is removed all of the (non-deep) ores except platinum, gold, silver, copper, and cassiterite, renamed mined cassiterite "tin nuggets" (I have no idea whether tin forms nuggets or not), and added a generic coal and iron ore. As I say, I've tweaked the frequency values significantly so there's a chance of anything showing up anywhere, but in general terms, metamorphic gets you lots of gems, igneous gets you gold/silver/platinum and bronze components, and sedimentary gets you more coal and iron. That should be simple enough.
As for flux, sedimentary and metamorphic currently have has the flux tag. Cluster flux is a really good idea, I'll add that.
I might also add obsidian clusters as well.
Edit: Stone's pretty much done. Moving on to wood now, then probably farming, and I'm not sure what after that.
Edit:
- All trees removed except tower-caps, generic tree added
- Kobold bulbs (gnomeblight), quarry bushes, and dimple cups annihilated. Most overland plants still exist.
Edit: Material-dependent creatures should work. Amethyst men are still called amethyst men, even if they're just made out of a generic precious gem. Precious gems made purple to compensate, as I don't feel like adjusting the creature.
Apart from that stuff, I think this is mostly done. Commencing testing...