really good review.

Germs - Good understanding on the hygiene theory. Its worth also adding that younger children get over sickness easier and probably won't have a memory of any pain of the process, so if you were to catch chicken pox - best to do it earlier in life. I personally believe in dirt and other exposure.

Lead - I don't know if you are aware but lead testing kits are pretty easy to acquire. Basic chemistry can help you figure out if a thing is lead or not.

Cats - I would say not to live with cats at all, especially not a small child. I know you think your cats are indoor cats, but a few experiments have been conducted on cats with collar-cameras which showed even the nicest of cats seem to manage to get out and eat things when no one is watching. I wonder if looking into this information will change your mind about the safety of living with cats. Part of me is very concerned about how much we don't know about what toxo does to humans. We know it makes rats more attracted to cats urine to encourage them to get eaten and pass on the toxo. I am concerned for the ability of toxo to get to the brain and modify it.

pets - certainly live with pets, I believe it does wonderful things for social-ness and empathy and companionship. (there is a vegan argument against having animals, but I believe it is important to have them), food animals - i.e. chickens - will help children understand where food comes from, as well as growing foods and herbs, lemon trees, and others add childhood memories to one's life. I personally keep bees, depending on your climate that might not work for you, and also the risk of stings exists. Having a personal model of a creature of a simple mind and simple behaviour is a good thing for building social intelligence brains.

IQ - I have no answer, but there is information that being more than 30 points away from your peers can be socially isolating and not actually lead to progress. If IQ was a good predictor of success (in various metrics) it would be more clear to be so. If you expect the world to change significantly to make this not a problem in the future then carry on, but I don't know how to consider limiting IQ to more socially productive levels.

Good Luck!

Edit: fish - I would trust some fish sources, i.e. river farmed, or private farm - depending on what they feed the fish and where the food comes from. also for the nutrients of fish oils.