Actually, the "organic feel" you're referring to is often a reflection of the strength and size of authority in a region, of the urbanistic precepts (or lack thereof) of the polity, of the economic and cultural base of the settlement, and so forth and so forth. For example, many European cities that were founded by the Romans were actually laid out on a very strict grid system, but the subsequent collapse of central power and the rise of the independent, walled city mutated the layout.

I would suggest, as a starting point, the terrain. Perhaps even a regional map, where we then determine where the new city shall be built. Then the questions follow: who is building it? how? how many people are there? what technologies do they have? what is their economic base? what is their culture?

Based on your wooden fort, I would guess a rather primitive, barbarian culture. Perhaps orcs or hobgoblins.