One of the hardest things to do in sports is build a culture of winning. Billion dollar franchises in the NFL and MLB have difficulty doing this. Look at the Browns.
Notre Dame's problem in men's cross country, in addition to the aforementioned sprinter head coach, is the erosion of a winning culture over the last five years. They operated with separate coaches for decades and the men thrived. When the new head coach combined XC programs, the focus of the distance coach went to the loaded women's team. So much so that he handed the men over to an inexperienced assistant. From those I talked to, the morale and dedication of the athletes was not good.
To Sean's credit he has put together two very good recruiting classes in a row as the head coach. Now he has to create the culture. It will be tough with no older guys to lead by example and no overwhelming coaching reputation of his own.
It has been done in recent years: Ole Miss, Syracuse and Furman were all bottom feeder XC programs 5-10 years ago.