Wow, thank you! It's kind of overwhelming trying to think of everything right away at the beginning; I'm really glad I posted this before I got too far! To address your points (not bored at all - the more the better!):
1) the coastline is pretty rugged and rocky in certain areas (I do need to clean the coastline up quite a bit), but the city actually "modern" rather than "old". I do like the old-style map, but the time period is supposed to be be pretty contemporary. So buildings can sit pretty close to to the edges of cliffs (especially in the older sections of the city, buildings are supported out onto/over the cliffs/rocks on stilts and such)
2) the zoomed in map doesn't show the oldest part of the city, which is over in that large bay area towards the east. There were several walls, around different expansions of the city, but they stop before that zoomed in section. I should definitely sketch in those walls before I get over there.
3) the point of origin is over by that large bay, where I need to put in a harbor. Which I should do so I can start setting up those radiating roads I forgot about! There are several old fortifications in various locations, which I also need to place.
4) I actually was planning on courtyards, but haven't started filling them in yet. At the moment I'm trying to hack out the "organization" of the city, before I start putting in the "smaller" stuff like courtyards and parks and such. I do, however, think I need some more plazas here and there, and definitely a more integrated transition from the more organized/"new" section and the older section shown in that section I've done so far.

A quick note on the canals - thank you for reminding me about the terrain question, and pointing out that cliffs kind of nix the canals idea. However, the city is approximately the size of Tokyo, so I'd love to see if I can fit them I somewhere. That'll have to be part of the terrain clean up.

A couple questions (for you, or anyone who's got some thoughts):
1) the area is pretty big, and it's an island - is it more likely for the city to expand from one point (like a harbor), or could people move out from the original town to a coast (maybe another harbor) or maybe to a more fortifiable location, and then those locations could expand out wards until they meet up/converge to form a whole city?
2) at the moment, I've got all the fields in the north; I figured that with city expansion, fields would be shifted out wards until they're on the edges of the city. In this case, they've been pushed into one area (I'll come up with a good reason for it, unless its hugely unrealistic). Is it more likely for fields to remain dispersed throughout the city? At least in the more urban areas?
3) because this is a modern/contemporary city (like Tokyo), there are districts that generally cater to specific "needs" (like Shibuya is known as a shopping district); I do want districts, but I'm wondering how much the "focus" of the district will affect things like streets and building size (and type, maybe). For example, the Tokyo district has a lot of skyscrapers because it's a business district, and it's got pretty straight streets. But the more urban district I lived in a few years ago had no skyscrapers (at least not anywhere I went), just a department store near the train station and some apartment buildings usually no more than 10 stories high, and the streets - at least away from the train station - become quite winding and often stop abruptly.

Whew! Thanks for all your advice and question; hope I've not asked too many in return! I'll clean things up here soon and put together a rough "outline" of where things might go.