Sounds like you've got a lot of promising ideas in there, Jake. If I may, I'd urge a small amount of caution in some regards:

- I like that you are including intra-mural farmland. As you have correctly noticed, many cities include this on their outer edges. This is because most houses in a medieval European town would have had a backyard that was used for small-scale farming, workshop, or both. As the land became more valuable, those would be converted into rental houses/shops with increasing frequency (I think I wrote this down in my earlier comment, too). Naturally, the central parts of town are the more valuable real estate, so they would convert their yards first.
- you want to add more chaos to the poorer districts: I'd recommend you steer clear of 'spaghetti' streets. It's a common mistake in city mapping, and it is neither historically realistic or (in my opinion, at least) visually appealing. Instead, I'd advise you to add chaos in the form of narrower streets, courtyards and backyards with more buildings in them etc. Going for right-angled dogleg streets is also a better solution than 'spaghetti'.
- regarding Melek's reconstruction, I'll just point out that many rulers in real-world history sought to redesign cities, and pretty much all of them stuck to the same formula: wide, straight avenues that link prominent landmarks and monuments, formal arrangements and layouts, etc. (eg Baron Haussman's design of Paris, Pope Sixtus' designs of Rome, Wren's designs for London - not all of these were ultimately realised).
- lastly, some of the grand plans of some of the above rulers were for practical reasons, too: Haussman's redesigns of Paris were post-Revolution, and he was building a city that would allow the government to fire cannons down the boulevards (or that's the version I've heard, at least). You could consider that when thinking about fire prevention measures.

Wingshaw