The amount of time they have been apart is not relevant to whether he can bring the suit against her for custody, but the amount of time that has passed since the last order relating to the children was entered by the Court is relevant. In order to file a suit within one year of the previous order and request a change in the parent with the right to designate the primary residence of the children, which is what most people mean by "full custody", he would have to allege that the children's current environment may endanger their physical health or significantly impair their emotional development. That is where the issue with the ex-boyfriend/roommate who has a history of theft and drugs comes in because the Court may hear evidence regarding the type of people she is allowing to have access to the children and decide that those sort of people could put the children in danger. Father's history of violence, especially if the restraining order is still active, could be a factor that would weigh on mother's side. Really, with the basic information you provided it is hard to give any sort of definite answer, but the short answer is that yes the ex-boyfriend/roommate is a problem and I would tell her to get him out of the house, if she were my client. Is the presence of the ex-boyfriend enough to get the father custody? I don't know because I don't know how bad ex-boyfriends charges are, how much interaction with the children he has, what other issues may be present, and how violent father is to mom and the kids.