You're trying to achieve quite opposite goals there, so you have come to one of the basic questions that leads to the three corners of designing crafting systems:
- Realism (in the context of crafting & economy, this means a high degree of complexity & depth)
- Usability (often this comes down to easy-to-use and not so much depth)
- Consistency (whether this part of the game merges well with the rest of the game system or whether it looks and feels like a bolt-on)
Think of these as a triangle graph: you can only have one or two out of three to a high degree. Either it is realistic and is somewhat useable, but risks not fitting the rest of the game, or it is likewise in depth — and then you play “Economymaster, the game where you need a PhD in history and economic to win”. Or you cut down on complexity a lot to achieve a useable system that's consistent with the rest of the game — just like the crafting systems in many games, which are pretty abstract.
Now, back to the other question parts:
1. What sorts of commodities and raw materials are out there and where to get them? A list of commodities would be great.
This in itself is a rather complex question. I could open my history books and start to read out lists of plants and ores that were mined at several points in history and would not cease to read out those goods for the next 3 years, but generally speaking we can break down the products into general categories. The most relevant categories I can think of, without starting to open books, are the combined raw resources, which can be broken down to roughly the following sub-categories (which in term can be broken down even more):
- Animals (live)
From these, most other goods can be made under the expense of workpower, which is kind of another vague category. Workpower could take the shape of free craftsmen, people hired by others, it could be slaves — but all have in common that some humanoid spends time and effort to refine the raw resource into some sort of refined product, which often has a more useable shape than the raw resource and again can be refined to take other shapes.
Think about this like the production chains in some of the more complex strategy or city building video games — Settlers 2 or Caesar for example:
- Ores get extracted from the ground in a mine, then get smelted into metal bars in a smeltery, then get shaped into tools and other metal objects in various smithies.
- Trees get cut, turned into boards, and then things get done with them.
- Crops get sowed, harvested, and processed so food can be made from them. Other crops get refined into fabric and then turned into clothes; others again jut get fed to animals.
- Animals in turn could be hunted or raised, then butchered for meat and hide, sheared for wool (which in turn can become fabric and clothes), or milked for drinking or making cheese and other milk products.
You see, already with these 3 basic categories — raw resources, refined products & workpower — the interactions become highly complex, and the more you break down any of the categories, the more complex the system has to become to cope with them!
2. How does trade and transportation (land and water) work, and what are the possible pitfalls of trading (taxes, bans on certain goods, robberies, etc.)?
Trade and transportation is again a topic people have written books about, especially in a historical context. Generally speaking, you would need to define what historical timeframe this economy resembles and then research in that direction in actual history books. I suggest looking into the history of the Hanse here. Generally, trade, transportation and taxation grow hand in hand:
If a marketplace develops somewhere, it is because people come together to trade, either bartering goods for goods or exchanging goods via currency (which is another thing you have to think about in terms of economy!). When people have to travel to trade, they have to develop some means of transportation for the goods. On the smallest scale, this could be a man carrying his goods to the market from his home. Or he invests and gets himself a cart.
Then, some crafty man might say "Mister Farmer, you lose a whole day of working your fields going to the market from your home to sell your load of wool for 10 silver. How about I come to your farm and I buy it for 9 silver, and you have the extra day to work on the land?" From this we get the first regional trader: he buys the products from the local area a bit cheaper and sells them at the normal price at the market town. Possibly he tries to sell a tad under the price of the local farmers, to deny them customers so they're forced them to sell to him instead.
This change however might lead to another development: if several traders start to do this for the same product, some have to go even further to gain enough goods, possibly crossing from the closer region (that belongs to the township) to areas that don't belong to the marketplace but some other. Those traders become overland traders, far traders. They buy in bulk from the regional ones, hoping to sell at profit further away where the product is not made at all.
With the growing number of far traders, some of the larger markets might want to protect their local products and get their share from the profits of these: They tax the import of foreign goods. And they want to make sure that their denziens get the first pick when it comes to goods transported through, and so force any trader passing through the area controlled by the market to stop and offer their wares.
Now, some large markets and towns might have the idea to try to benefit from forming an alliance — the traders from those towns get special privileges (like less or no taxation, or not being forced to offer the goods) in the other member's towns: the Hanseatic League or its equivalent is born.
3. Crafting! How would you proceed in creating this sort of a complex, multilayered system, where raw materials are being converted into more polished materials using various vocations and techniques (which ones?)? How would you design a crafting system, where these commodities and materials are used to assemble finished products? How to fit in the price of labor, and the skill of rare artisans?
Well, I ended up answering this part before the others, so... just read above?