Well, as I said before, it would be quite easy to replace the rice with Corn as the food bonus resource, and it would even have some Final Fantasy Canon involved: One of the food items (for restoring health, etc) in Final Fantasy Crystal Chronicles was called "Round Corn" (basically corn with short, fat ears that were about as wide as they were long), and IIRC, Corn showed up elsewhere...
It's either that or Gysahl Greens, which show up in all but a few of the games (and in FF IX, they were eaten pickled)
Also, the sea serpents replaced the whales, but I could put the Whales back in, since, now that I think about it, Whales (and dolphins) actually appeared in more of the FF games than sea serpents (Leviathan, excluded), but I am NOT using the default Firaxis whale resource... If all else fails, I'll convert the one from Civ II ToT...... It was much better looking, IMHO.
I was attempting to have all the resource buildings as a way to make certain aspects of the game more interesting... I.e. using HN units to raid enemy trading (stealing their treasures), and as a way to get some quick gold for your resources....
Although You're right about not having a building for all of them... I suppose only the ones that it would make sense for or would actually be trade commodities...
So that brings it down to these, then:
Iron: Foundry (makes sense, and I could even have a foundry a prerequisite for building the Bastok Metalworks SW, which currently requires Iron in the city radius anyways)
Materia: Makou Reactor
Hot Springs: Already has Hot Springs Resort and Geothermal Plant
Relics: Archaeological Dig, which can serve as a prerequisite for a Bone Village Great Wonder (I even have graphics prepared from when I was thinking about adding that earlier, but never gor around to it)
Mythril: Mythril Mine (definitely makes sense, since Mythril is so valuable)
Coal: Coal Mine (again, makes perfect sense)
Chocobos: Chocobo Ranch.... No ifs, ands or buts about it either: This one's definitely canon, and for at least 3 games in the main series, too!
Gems: Gem Mine (again, a no-brainer, here... Gems are valuable, so having some kind of special improvement for them makes perfect sense)
Spices: Spice Market, again, makes perfect sense
Silks: Silk Weaver, Again, having this luxury produce a treasure makes sense, due to how valuable silks are
Here's an updated probable Bonus resource list... Gotta scrape up the Corn Resource (convert it from ToT, actually), whales and Qu Village, as well as modify the fruit resource (use my converted quench fruit from the ToT sci-fi scenario), and
steal grab the pearls resource from the Warhammer mod:
Game
Cattle
Corn
Gold
Exotic Fruit
Oasis
Sugar
Moogles (boost production and trade in forests)
Qu Village (boosts food and trade in Marsh squares)
Farm Village
Whales (sea and coast)
Fish (sea and coast)
Kelp (sea and coast)
Pearls (coast)