there are more questions to Ishual than just breeding stock. Carrying capacity of the valley, how do they hide agriculture from aerial observation, do they have aquaculture as well, what about livestock? Where do they get the animal fat to make their seeming infinite supply of candles? they clearly don't hunt, which is bizarre (they're simply too tall and too strong to be vegetarians). why have they maintained smiths and iron/steel working knowledge? Do they also mine ore? How do they make clothes? Even maintaining a self sufficient community of 1000 is tricky and involves an enormous variety of specialization and skill sets in just providing basic necessities. I presume that since Non Man mansions are so ginormous that beneath the Thousand Thousand Halls is the actual non man mansion, and since non man mansions were able to sustain subterranean communities of vast scales, there must be some ways of aqua culture, agriculture and animal husbandry etc that can be done deep in the bowels of the earth. and it's down there that Ishual really is, all unbeknowst to Kellhus because he never thought about where his sword came from, where his clothes came from, where his food came from etc. He was your typical privileged git, totally ignorant of everything that provides for his existence, all those come before him. 
All very true. Ishual must have been much more than a Castle on the side of a Mountain. They might not have had much experience with metal working, since who knows what riches might remain in the bowels of a Mansion, and I doubt the lose many artifacts on expeditions south. A nonman armory might be large enough to supply the Dunyain with all their metal-worked goods for thousands of years.
The problem of food an hunting are much more important though. Maybe they just had all the 'failed' Dunyain preform all the menial tasks, and they left all the philosophizing to the brilliant?
I've heard investigations into human genetics have suggested we were down to a near extinction level of only two thousand individuals in the distant past.
So were all pretty much inbred right now, (distant) cous!
This is part of the problem I didn't really bring up (or maybe I did and forgot). There must be some critical mass of genetic data that leads to increasing diversity overtime, rather than decreasing diversity. I wish I knew what that number was, but in absence of that I was just trying to figure how to keep the Dunyain from being a bunch of autistic hill-people after a few generations.
Being 'related' to someone is a vague qualifier at best. I wish I knew what % shared genetic data qualifies individuals as 'related' such that there is a high chance of birth defects in offspring.
