I don't know if you've seen these. They might help.
Mississippi State Incubation Troubleshooting
http://extension.msstate.edu/content/trouble-shooting-failures-egg-incubation
Illinois Incubation troubleshooting
http://urbanext.illinois.edu/eggs/res24-00.html
At a seminar a poultry science professor specializing in reproduction said if the eggs died in the first week of incubation it was generally something that happened before incubation started. If they die in the last week, probably something to do with the incubation. Not always but probably.
Before incubation could be how long they were stored and conditions they were stored in, how they were handled, and health and nutrition of the parents. I'm not that up on lethal genes. It appears most of them cause death later in incubation but that young is possible.
That same professor said ventilation isn't that important early in incubation so I really doubt that was the problem. As the embryo's develop they start breathing inside that porous shell. That means they are breathing in oxygen and out carbon dioxide, just like us. So later in the incubation and especially after hatch they need good air exchange. That's not your case.
Yes. I'd have to search and find photos to say when but pretty young.
Heck, I don't know, see above. I don't know what you did but getting quitters isn't that unusual, either in an incubator or under a broody.
This is a common misconception. Whether the embryo is developing or not has no bearing on whether bacteria gets inside and starts multiplying. If the embryo is developing, the bacteria kills the embryo and it stinks. Since none of the eggs have bacteria developing inside you did well on cleanliness.