My other character. Changed.
How much space is needed for a sanctum and laboratory to be considered decent-sized?
With 4000 square feet + the 2 smaller houses I think we have quite a lot of room even for some of the grogs.
Here is a very rough suggestion for room allocation:
Big house 1:
Council Hall
Library
Sanctum and lab for one magi
Big House 2:
Sanctum and library for three magi
Small house 1:
Kitchen and living quarters for 1-2 grogs.
Small house 2:
Living quarters for 4-5 grogs
A standard lab is 500 square feet. So you can fit 2 labs on one floor of the large houses.
That is separate from the living quarters of the magi, but how much space that would require is really up to you. It can range from just a small bedroom (about 80 sq.feet) to a full-blown suite with a large bedroom with a personal studio or meeting room (250 sq.feet or more).
Just for additional reference, a modern meeting room for 10-12 people is about 200 square feet.
Note that for the villagers, one of the smaller houses is enough for a whole family of 4 to 10 people (often with some livestock). Medieval living standards are much more crowded than what we are used to. One of the reasons is that it preserves warmth in the winter. And in the summer, most of them are working outside anyway. Of course, for peasants a house is a place to eat and sleep, not work.
EDIT: A lab can be smaller than standard without too much impact. If we use the rules from Covenants, it just means it will have a minor flaw, which can be eliminated by spending an additional season refining the lab.
EDIT 2: If the kitchen is away from where the magi will be eating, expect some lukewarm meals in the winter and grumbling kitchen staff.
EDIT 3: The small houses are about 500 square feet in size, giving you a total of 5000 square feet to play with. Plus whatever space you dig up as cellars. Note that diffing up cellars after the building has been erected is riskier, as it can undermine and weaken the building's structure.
Here are some very simple drawings of the floor plans of the two larger houses. As a suggestion.
The labs are only accessible by stairs from respective sanctum.
I have not included the cellars but I think the stonemason should excavate those first and then use the stone as parts of the construction material for the walls.
Ground floor House 1:
Upper floor House 1:
Ground floor House 2:
Upper floor House 2:
That works for me. Thanks for drawing it out.
Dietlinde mentions that having that many people eating in the kitchen won't be practical. Perhaps the room labelled "Guest room" in the second house might be better if it was a hall. Perhaps even merged with the hallway, or simply seperated by an archway of some sort.
How would the hearth be arranged? You were granted the rights for six hearths for your community, as per the document Dietlinde obtained for you. The small houses each require one each, so that leaves only 4 hearths available for the large houses.
And a lab / sanctum without a hearth will be quite cold in winter. And we have to have a hearth in the kitchen, I presume?
If we have one chimney, with two fireplaces (say in the sanctum and the laboratory) does that count as one hearth or two?
There shall definately be hearths but I didn't include so much detail. Two chimneys per large house then?
My thought with the kitchen/dining room was that it may be divided by a wall. I made the ground floors look the same in both houses and just changed the text.
The sanctums are about 200 square feet each, the other bigger rooms might be 250-275 something. The entrance could be directly into one of the bigger rooms and then the hallway could be diminished to a smaller area in the middle.
If we can get away with two chimneys, but multiple locations that get heated, then that is fine. I don't know how the "hearths" limit was understood in that place and time.
Hearth ≠ chimney. In most peasants' houses there is no chimney, just a hole in the roof.
Every fireplace is likely to be counted as a hearth by the tax man.
Then it seems what we have to do is set up a hearth in the kitchen, and one in each laboratory, and for now we each plan to use our lab as our living space. Set up the bedrooms so that if we can arrange to heat them we can use them later?
Are the plans posted previously the ones presented to Lothar?
Yes, the plans posted previously are the ones I was assuming Tristan presented to Lothar. I was looking at them and the notes around them for the discussion.
It's just that I notice a few things that are missing from those plans. So I'm giving you all a chance to correct them before construction starts.
As I mentioned before, there is the matter of the hearths. With 4 hearths left to assign to those two houses, it won't be enough to have an hearth in each lab, unless there isn't any in the other rooms (like the kitchen). So I think it's Worth deciding how the magi want that handled. Of course, if the magi aren't too involved in the construction, the end result might be that there is no hearth in the labs... :mrgreen:
There's at least one other feature of the houses that have been left out from those plans, but I will leave it up to you (for a little while at least) to find out what it is before giving you a hint. 
I had explicitly included a question for Lothar as to how to handle the heating. We do not have the vis to create magical solutions for this, and possibly not even the skills. I don't know how larger houses were kept warm in this ear unless they had hearths, but I bet there was a partial solution somewhere.
the only answer on that I had come up with so far was to figure that for now, the magi use their labs as their living space, and we build three labs with hearths and one kitchen. That does seem to mean that the meeting spaces will get COLD in the winter.
I presume Lothar will eventually ask for confirmation that we plan to use outhouses for "waste" disposal.
Lothar might have a few ideas indeed. I'll list a few that he might suggest.
Shared hearth is one possibility. Have adjoining rooms with a single hearth between the them. Basically the hearth has no back wall, so that when there's no fire you can look into the other room. This reduces privacy, but there's nothing preventing you from closing off the hearth when there's no fire burning in it. Or installing a privacy screen in front of it.
Using an hypocaust for heating would make for a more comfortable building. But that is a much larger job, particularly for a single stonemason and his apprentice. Would make building each of the large house much more expensive and long, more than doubling both time and cost. Lothar's never done a job like that. He'd be eager to undertake it, but isn't sure how much time and efforts it would take, nor how well the system would work.
Use braziers in rooms that ddon't have a hearth. Ventilation might be a problem however. The cost of heating the houses would be a bit higher, but it has little in the way of initial costs or delays. It is also a bit of a safety hazard.
Arrange for the right to additional hearths. This may mean an additional bribe and contact with the officials handling that.
It gets quite cold in the winter indeed. But the villagers don't have houses that big, and they're mostly single-room houses in any case, with a central hearth. It's drafty and not very private, but such is the life of peasants.
They also keep some of their animals inside their house. That adds to the heat of the fire.
The main problem I see is the library. If it were not for that, I would say put Hearths in three labs, put the chimney through next to the fourth lab, but don't put in the hearth there yet. Then use a brazier for our meeting room and when needed for the guest room.
But that leaves the library unheated, which seems a problem.
So what if, for now, we use Sanctum 4 as the library, since we won't be using lab 4. We put a double-hearth in there, with a metal safety screen to keep the embers out of the library?
When I drew them they were just intended for ooc use to help give us some mutual understanding of the distribution of rooms. I didn't include hearths and privys intentionally just because I didn't want to go into that detail.
So I think the magi may have done a little more detailed version to present to Lothar before he arrived. Japik is not the most responsible person so he may have left it for the other magi to decide after the general plans and ideas were discussed. If these plans are the actual plans Lothar gets then he will freebase a lot. 
He would probably see them as rough drafts of what his customers want. So he'd probably draw new ones, more complete with annotations about supports, arches, hearths, cellars, etc. These would be some of the details he'd ask questions about.
Privys we can handwave. At the time there was seldom anything like a special room for that. Most would simply use a covered bucket, which the servants would take out, empty and wash every day. On a place like the plateau, the buckets would be dumped down the cliff (probably over the sea).
Another thing he'd have questions about is roofing and flooring. He's no carptenter, so he'd expect there would be one to take care of that. It's doubtful that the simple roofes that the villagers use would suit the magi. That's what the small houses have, and it's drafty and doesn't retain heat very well in the winter. It also needs to be replaced every year or two, exposing the interior to the elements during that time (a few days). For the large houses, that would be the labs, so you can imagine how that might disturb any activity going on during that season.
(Answering here because this is a bit long and I don't want to clutter the in-character story too much.)
Low end wouldn't add anything to the costs already estimated for the large house. This is much like the small houses are built. It is drafty in the winter, with some leaks when it rains in the spring and until the roof can be retatched during the summer. There is some maintenance cost, in the order of half a pound of silver every year.
High end would be something like a slate tile roof, backed with planks (instead of just interwoven branches). That can almost double the cost of the house (adding at least 10 pounds of silver) but is much more wind- and water-proof. Maintenance is less frequent, as most years there is not much to be done. But occasionally some of the tiles may crack or fall off, which requires more costly maintenance (1-5 pounds of silver).
In the same way, one can invest more into the carpentry for the inside of the house for floors and stairs, over what the basic cost requires. This creates a more comfortable living space, with floor that don't creak as much, walls where one cannot peak through cracks, and other small things like that.
Depending on how much silver the covenant adds to the cost of construction, I will assess that the characteristics of the house will be (structural flaws and/or virtues). There is some chance involved there, with the additional cost acting as a modifier to the die rolls.