I've just talked with Zax the supercomputer and I think i could make this work.
The idea that they need the people in my Vault makes sense now. I'm not sure of the exact line, but it says that if it is injected into a person with genetic damage, like from radiation, it results in massive overhauling resulting in organ damage and death. Zax doesn't seem absolutely positive about transmission of the virus. He says something like "Typically, you need to be injected or dipped."
I don't see why anyone would care that the mutants were sterile. They could have kept a group of humans as "hosts" (Children of Catherdal, anyone?) They would let the humans reproduce, in controlled conditions, and make them mutants. The mutant population would have a very low death rate, because "cell death would be offset by augmented growth"
Remember. Zax was cut off from the outside world for a very long time.
Those infected by the FEV virus became super smart, but might not have been able to unlock all of its mysteries.
I admit there are inconsitencies with the plot, but the creators of Fallout, in theory, could explain away everything. Just because someone says something doesn't mean it is fact. Esp. in a post-apocalyptic world.