Hmmm... I think you're putting the cart before the horse here. For instance:
Quote Originally Posted by SteelyGlint View Post
The first goal is to determine how important each city in the world is, since in the real world city population size was highly linked with how much of a hub of trade a city was.
This is, at best, a misrepresentation of where population size comes from. Many 'trade hubs' of the Middle Ages (say, Lagny in Champagne) were seasonal trade fairs and never functioned as cities. Many cities (or, at least, settlements) had political power because the local lord was important and powerful, but were never trade hubs (like, say, Lusignan, also in France). The force that makes cities more and less powerful (and, peripherally, larger or smaller), at least in the long term, is economic development, which is symbiotic with but orthogonal to trade.

Quote Originally Posted by SteelyGlint View Post
Initially, I want to procedurally determine the population level of each city before the game starts.
Again, city sizes are dependent (somewhat) on economic development -- the more things are produced, the more people can be supported doing something other than growing food. This means that city sizes are highly historical. Still, you could do worse than draw sizes from a logistic distribution and fake a consistent backstory.

Quote Originally Posted by SteelyGlint View Post
As the game progresses, I'd like cities to slowly wax or wane in power based partially on how involved they are in the flow of trade. ... So, how do I determine which cities prosper due to trade? How do I determine which nations (groups of cities) prosper due to trade? How can cities or merchant organizations attempt to control trade to their advantage (naval power)?
Again, begin involved in trade is less of an issue than economic development. Basically, it comes down to four (and one bonus) steps:

  1. You export something. Initially, at least, this is usually natural resources (mined silver, sea fish, salt, whatever). Being able to export means that you have more than you need.
  2. You can thus trade your exported goods with other cities (via merchants, trade routes, what have you). You buy things you want (or need), that you don't produce yourself.
  3. The key to the process is that it's cheaper to import the raw materials and process them yourself, than to import finished goods. So you see things like the development of a fine Flemish textile industry, replacing the importing of linens from southern Europe. This in turn has two effects:
    1. You no longer have to import linen.
    2. You can now export the textiles you make.

  4. These two factors mean that your city is bigger (by all of the textile manufacturers, and the people who make their shoes and candles and...), you can import something in lieu of the linen, and you can import even more stuff by selling your textiles.
  5. The additional bonus is that some of the textile manufacturers might now branch out into other fields (say, decorative lace) and you have have even more exports.

I've tried to work out a way to simulate this process procedurally, but it's extremely difficult due to the fine-grained nature of the goods you have; basically, just having "precious metals" or "fine timber" isn't enough (what about the craftsmen that make the jewelery or build the oak-beamed manse?), and lumping all "luxury goods" together completely ignores the creative side of the process. Without economic development, trade is just "buy low - sell high", which can be a fun game, but is pretty much completely solvable (with something like solving a Walrasian system of equations for the equilibrium prices).

So, in short: The process of "trade" can be broken up into static and dynamic processes. In the static simulation, it's pretty simple, because what is produced where doesn't change; even fluctuations like land routes closing or cities being besieged will have only short-lived effects. If you want trade to affect the economic fortunes of cities, you need a much more fine-grained analysis, simulating the economic life of each city, and allowing novel goods to appear; this is difficult to do.