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When I say self-eliminate, I refer to the idea that her eggs won't get hatched--her genes won't be passed on. I simply won't set any of her eggs

So far there have been enough distinct differences between the eggs that I can differentiate. I keep the newest eggs separate. If a bird goes broody I select the eggs I want her to hatch. I mark them and remove any eggs that aren't marked. As the numbers grow that system will probably get...

Sure, but broodiness is part of my goal. At this point the eggs are a side benefit. Any hen that just stays broody is going to self-eliminate. Any hen that doesn't go broody at all will also self-eliminate in the long term.

Right now I am breeding for crosses, but once I have the clans set I'll let any broodies set ONLY their own eggs. So the only genes that will get passed on are from broodies.