MCC, you should create some sketches or diagrams to show the direction you're heading in. In the meantime, though, I've had a few more ideas:

--the turtle is the main platform for this city, but the city does not need to be limited to the turtle only. The inhabitants could also have extensions of the settlement on rafts that drift behind the turtle, on nearby ships/platforms (or other turtles, as Neyjour suggested), or even underwater (clinging to the turtle's belly, or floating freely, but tethered to the main city) if they have a waterproof material. By allowing the city to exist beyond the confines of the turtle alone, you can make the best use of the limited amount of construction and farming land (as I said before, old cities don't need a lot of space, so I imagine farming would be the key).

--defence: how safe is the city? It seems a bit like a silly question at first (a moving town is automatically rendered some level of protection) but it probably wouldn't be too hard for pirates to board an undefended city, and trading success always makes something more of a target. My suggestion: the inhabitants wouldn't rely on walls and towers for protection (they are clearly going to be impractical to build and maintain in the circumstances), so a strong and fast navy would be the first line of defence (if I was running things).

--even with a navy, you wouldn't want to leave things too much to chance. A fortified position might be the smart move, and if it was my town, I'd give the lighthouse some fortifications.

--water: I don't know where the inhabitants get their water from, but maybe they could create enormous waterproof sacks that float beneath the turtle. They wouldn't significantly slow the turtle's movement, and they could provide secure cisterns. Also, the natural runnels in the turtle shell could be used to the advantage of water collection and irrigation.

--it seems probable there would be people whose jobs are to tend to the turtle (cleaning it, removing parasites, perhaps tending to injuries caused by other animals or accidents). Furthermore, there would be people who need to spend a lot of time underwater. A lifetime of training can let people stay underwater for long periods, without any need for technological assistance.

Anyway, I'll leave it there for now.

THW