Remember that during the time in which she is illegal, she is subject to detention and deportation proceedings. This will further complicate her processing. If she leaves the US during the period before you may file for her, even her marriage to a US citizen will not automatically override the ban she incurs on the basis of her overstay.
The processing time for naturalization process can be over a year in some locations. Therefore, do not expect to be able to file as soon as you meet the time requirements as there are additional delays you will encounter before you are able to take the oath.
You can only file as a LPR if she is eligible to adjust status which she is not because she is an illegal overstay.

