Well, first of all congratulations on the residency. Luckily you're definitely not the first to encounter the living-apart-before-ROC-issue. Found multiple older threads on the same topic, see one of them just below. Explain the nature of the residency requirement to the USCIS - location is non-negotiable - and the reasons why she can't move with, and support that with evidence of maintaining for instance shared bank accounts and trips back and forth every now and then. You should be fine just make sure you collect a lot of evidence of continued marriage.
Cormac got a reaction from nullaccount234 in Random situation