The river does flow W -> E. The docks were put in up river to give them more protection from raiders. Most of the "ships" are more along the lines of rowing vessels than tall ships, and thus would be able to fit under them if needed. At this time in the world, cross sea voyages are non-existant. Everyone pretty much stays within site of shore.

There will be a few more roads, the main road to the SW I already have the base for, there's one main gate on the NW side. Smaller ones that will have roads coming from them on the NE and SE sides.

There won't be much in the way of Suburbs; as the planning for the city left quite a bit of space to be filled in as the city grew; but there will be some that will dot the roadway from town. However, what you mentioned about the smaller markets outside the gates I hadn't really thought about; so I'll have to take that into account now.

I'll have to take a look at some of the older maps of London and see what I can learn from them.