Apply right after the marriage. Don't wait ninety days.
The feds make things up as flat out power grabbers. There's also immigration laws that make her immediately able to declare herself a RA. But look, I'm interfering too. Do it their way and avoid their spoiled children tantrums.
Best wishes to you both.
I think you seem to be missing something.
See, we apply for the fiancee visa, which takes 5 months at least on the US end(took 6 months for us). Then her country has to approve it via interview(to make sure she isn't horribly sick or a paid prostitute or something). Then she comes into the US, we get married, and then she can apply for a change of status from Fiancee to Resident Alien. Since the process of being a resident alien has mostly been completed by the fiancee visa process, she can not only stay in the US while it's being processed, but it's almost certainly a guarantee that she'll get it and relatively quickly.
Then she'll get a green card which will allow her to work in the US.
Contrary to the movies, getting married to a US citizen doesn't automatically make you a US citizen.