One way that freight costs can be done is to set up several Centers of Trade (it's not perfect, but it reduces the processing requirements). The game can then assume that all provinces trade through their center, so each center has a certain price for each good, and the provinces add a certain amount based on distance and railroad levels.
We can then simulate long distance trade by having firms that purchase goods in one center to sell them at the other, at a cost based on distance and the price of either steamers or clippers, oil or coal, based on the time in game. This would allow prices to equalize to a world price, based on the actual costs of shipping. The shipping company shouldn't be too hard to simulate once you have separate markets; you can simply have a factory that uses a good, ships, fuel, and labor as inputs to produce the same good as an output in a different market, although it would be better to do it a different way since that technique would require an enormous amount of factory slots. Rather you can simply model a shipping company between two slots that consumes ships, fuel and labor to get its operating costs, and then is able to trade between markets whenever there is a large enough price difference to make a profit.
Note that this would also create a real purpose to tariffs, since it would actually impact trade in a realistic sense.
It would also be cool if the market could simulate factory ownership, so some factories are state owned and some are owned by capitalists or even workers; the fate of capitalists will be tied to specific factories rather than industry as a whole in a region, and workers who own stocks can supplement their income or even promote to capitalists if their stocks make enough money to quit their jobs. It would also enable the implementation of a firm system in which a single corporation can own multiple factories (and in turn be owned by a set of capitalists around the country). Especially in industries that face high shipping costs, this would enable us to see the monopolization and market power that was common in real life during this time period.
Moreover, it would allow us to more accurately model technology; technology can be split between ones that are researched by the state and ones that are researched by firm's in the market (as many technologies and inventions in this time period were). This creates an organic tech lead for countries with an active free market containing many clerks, which historically happened, and enables the research of multiple technologies at once. It would also allow the player to choose to set up state owned companies and pour government money into an industry like arms manufacturing in the hopes of encouraging technological breakthroughs there, although state owned companies should have a penalty to research efficiency.
