Clonay parish is likely to be spelt Clonea. It may refer to the parish of Clonea Power - a book on this parish was launched recently http://blog.waterfordmuseum.ie/2010/07/new-book-on-clonea-po...
If he was RC, he may have gone to Mount Mellary in Co Tipperary - this was a Cistercian monastery which prepared students for the priesthood at one time. The Kill college is possibly St Kieran's Seminary in Kilkenny. This is now a second level school. If you check the 1901 National Census, there are some Greys/Grays in Mothel. The Griffiths valuation of 185-60 has a number of Grays in Mothel.