As i was working on the city level I started thinking of some of the residents and magic items for the sanctuary... Here's a few off the top of my head...
-Gwidion of Verditius (from Magi of Hermes)
-the enchanted plants would be a great way for water, light' and fresh air to be moved to all rooms.
-Rats Magica (from Sub Rosa #15)
-at first I saw the mage rats as a kinda computer doing research. But the after i thought of Gwidion's enchantments i could see the rats as those who care for the plants and make sure pests dont destroy them.
-The Cult of Memory (from The Peripheral Code #3)
-could do Harry Potter style paintings or sculpt busts to animate.
On the far left are 3 theatres for debate or plays.
There are some labs near the wizards quarters.
There are also grog quarters and 2 bathhouses... The large cave is for an artificial forest.
Just a comment. With the number of Magi you are building for, unless you're ditching the rules in Covenant, I don't think most experienced magi would be content with a Size +0 lab.
Have you checked out “Hermetic Projects” and “Transforming Mythic Europe”? They have examples of creating a new island from scratch, and building a tower as tall as needed. Good examples of spells and items to make construction easier.
Counted the number of labs (283), mage quarters (432), and non-mage family quarters (410).
I have rough ideas for 3 more levels:
1- Farm level (also has mage quarters, labs, and farmers quarters)
2- Treasury level (vaults for silver and different vis (need to look into ways to prevent mass amounts of vis from being unstable) and a ton of labs)
3- The Dock level (docks and warehouse space)
Let me know if there are more specialized areas needed...
How about some type of freshwater lake? for all those freshwater fish/plants that a magus may be familiar with. If this tower is out in the ocean they don't want to travel too far to get any necessary "supplies" for their research (and food).
A level with open ground and lots of strong wind blowing across it. Perfect for indoor birds, auram magi and of course, laundry. Nice place to exercise the grogs too.
A special place for magi to do dangerous research or test new spells. Lots of enchantments on the surrounding walls to make them stronger, lots of PeVi spells and circular wards.
Not sure if you mentioned any stables or other areas for familiars, livestock or domesticated animals.
You could also do with some areas for magi to install portable vis sources. moving entire graveyards that generate corpus vis etc. Not all vis sources can be moved, but some of them can be (with appropriate research)
If you think of having 160 wizards, consider this question: How do the Study Requirements magi study, in this covenant? It's a question you can ignore with 4-10 magi, not with 100+.
While reading other rpg books tonight i was hit with the idea that once the sanctuary is built it could be used for hermetic fairs and tribunals. It would also house warehouses for redcaps and a museum.