2 dead at 3 days of age from a hatch of 40 is completely normal. There are always some that don't make it. If it was 5-10 from a hatch of 40, you were likely doing something wrong, but 2 is basically unavoidable.
Boinking is flying up and hitting their heads at the top of the cage - as they...
Lethal genes usually mean the chicks never hatch or die very soon after hatch.
Breathing hard could indicate an airborn toxin - carbon monoxide, over heated non-stick cookware and self cleaning ovens are possible culprits. In particular if several birds died at the same time. Otherwise, boinking...