I've got some general questions/comments that thinking about might help you with your worldbuilding aspect. I'll break it down by color for ya.
Yellow/Uptown - This one is particularly interesting to me. I see two ways this land can develop over time, as it's the closest to the large skirmishes. 1) It get's overrun with fighting year after year and eventual ware and tear slowly make it just as bad as the slums. This could be where those rundown mansions you mentioned earlier reside. Also, a lot of people would probably leave their older-style homes in this part of the city, buy cheap land in the original "slums," and start pumping money into their new neighborhood instead. This would allow you to have clearly contrasting architecture between the "old" and "new" as the players walk from district to district. This would mean Uptown has taken a downward turn, and the slums would likely be on an upswing (or become even worse as it slowly overpopulates).
Alternatively, 2) The residents double down, pumping tons of money into that part of the city to beef up security and protective. More guard patrols, better quality walls along it's borders, and likely a larger sense of city pride from the resident population with each successful assault protected against.
Navy Blue/Guild District - Do you know what guilds reside in the city? Could a PC potentially join one of these guilds?
Pink/Cliffside - Is the coast along Cliffside an actual cliff or just a name? If a cliff, how steep of a drop? Are there rocks below? Could a PC survive the fall?
Red/Slums - Revolutions can be fun (And see my notes about Yellow/Uptown).
Teal/Docks - Who/what holds the largest monopoly over the docks? Is it a political figure? Is it a guild? (It could be a political figure giving his guild large tax cuts when using the docks) If you do want to go down this necromancer route, were the necromancers working/being controlled by the Aboleth, or do they have their own sinister plans and saw the chaos the Aboleth was causing as a good screen for their operations?... Ooooor whatever else you come up with.