Expired visitor's visa married to a lpr adjusting status in the u.s.

[papillon]

My wife came to the U.S. on a tourist/visitor (B1/B2) visa 2 ½ years ago, we decided she stayed with me and we get married a few months later. I am a LPR and I will qualify to apply for citizenship in Aug 2017. I filed the I-30 for my wife, and after waiting for over a year she finally got to her priority date, and right after that we submitted the I-485 for her adjustment of status to LPR. We recently, received a letter from the USCIS requesting evidence that shows that she had a legal status at the time when the applications was first submitted or to complete the form I-485A with a $1,000 penalty fee. After reviewing the form I485A, we realized she doesn’t qualify to complete that form, but at the same time her I-94 had also expired when we first applied with the I-130. They gave us 90 days to submit the evidence so we have until July 1, 2017. I have gone over some information that tells me if I was a U.S. we could resolve this issue with no problem, I won’t qualify to apply for citizenship until within 4 months and I probably won’t have a citizenship until at least 4 months after that. I don’t want her case to be denied and probably risking deportation of my wife. What could be a possible solution to this case? Please help me!