Greetings…
Well, here’s the thing. Regardless of what setting you borrow from, or outright use verbatim. Once you put your fingerprints all over a setting it’s going to become uniquely yours. Now, I would definitely recommend Ars Magica, Harn and A Magical Medieval Society: Western Europe as others have suggested here. Personally, when I got around to reading aMMS:WE, there wasn’t much there that I hadn’t worked out for myself by reading wikipedia, history books, and Ars Magica.
One of the better books talking about medieval society in the Ars Magica line is the book Ordo Nobilis. I’d give you my extra copy, but I don’t think you live anywhere near me.

Actually, I don’t know if they still do this, but before you could pick up Ars Magica 4th Edition for free online. DrivethruRPG.
But my suggestion is, read what you can, learn about everything you think is important/interesting, and move on from there. Because your setting is only going to be as good as the amount of research and effort you put into it. But don’t too much work, just do enough that your players will be sufficiently impressed. Because the last thing you want is to do too much and have your players be completely uninterested in such things.
But if you’re writing generically, for everyone… I would also suggest the complete opposite. I am of the mindset that if you’re going to design for public consumption then make sure you be as detailed and through as possible. Yeah, sure not everyone is going to be interested in the fact that the farmers in and around this village mostly grow sweet corn, where the next village over generally grow beets and cabbages. But then again, someone out there probably will want to know such things. I say its better to write too much, and have too much detail, because your readers can always ignore it, or turn it into something useful for themselves. But, they will crucify you if you don’t put enough detail. It just looks lazy that you didn’t make the effort.
Like grodog, Ars Magica is probably my favourite RPG as well. But only for the setting. The rules themselves, for combat, are horrible. But other aspects of the game I thought were brilliant. They use something called ‘troupe-play’, where each player may have two or three characters, which was interesting. But the thing I liked the best was the idea that a party of characters aren’t a bunch of homeless adventurers, that the important characters are members of covenant of magi, and generally trouble comes looking for them. This is something I usually try and do now in all my RPGs that I run. That I will give the players a pretty good and strong reason to want to live in one particular location, and if they want to travel and wander, that’s completely up to them. I just find it more rewarding (roleplaying-wise) when you can develop long-term relationships with common NPCs.
Griffith, sounds a lot like my own game world. But then, aren’t all the best materials taken from history? Though, I have a different spin on my royalty. I have adopted the idea of the Merovingian kings. (I love a good conspiracy theory – my friends love/loathe my pulp/modern games that revolve around modern conspiracy theories) Also, I have a church that is gearing up for an inquisition on steroids, and if everything goes wrong… a crusade. But I’m thinking small, and thinking of only doing an Albigensian crusade. Nothing too big, staying in one’s own country. Though, I don’t do the whole law/chaos thing. I have reworked the whole detect good/evil. I also have the potential for dwarves to become the religious/social pariahs of my game world, and persecuted like the jews.
In my game world, the main human religion (in the one country I’m concentrating on) is a religion that evolved from the dwarves, and the progenitors of the dwarves; a race of ‘proto-dwarves’ that were slaughtered by the elves in a great war, known as the zwerg. When the zwerg were slaughtered the gods took notice and stepped in to curse/punish the cyndar (elves). The dwarves eventually became a race that depended upon the humans for their protection and survival, yet always mainly lived on the outskirts of human society in the hilly and mountainous regions.
Coherence is a very tricky thing to achieve. Personally, when I first looked at Dragonlance or Forgotten Realms, I thought they were slapdash. But I’m sure to others it was the greatest thing since the invention of the icosahedron. The only ‘perfect’ medieval setting, I dare say, is the one that mirrors our own history flawlessly. No matter how you look at it, your setting is always going to be a collection of ideas. After all, are you considering the migrating pattern of insects that would ravage the crops of a particular region, and how that impacts everything from the wildlife, to monster habitats to the amount of crops that the serfs are able to harvest this year, as well as how this impacts their liege lords and ultimately the king and kingdom? Probably not. Who wants to do that much work?
By the sound of your setting Danyæl, it seems you have a relatively advanced world in regards to technology and architecture. The only thing that doesn’t seem all that logical to me is ‘outsourcing’ a town to build siege-weaponry. From what I know of siege towers/weapons, most were built on the spot. Since it would be an incredible task to transport such an object to the location that it is needed.