Here's Paul MacCotters' impressive list of references he used in the project.
Affairs of Ireland before the Kings Council Analecta Hibernica (periodical, 1933-) Annals of Ulster Beathaisneis iii Begley's History of the Diocese of Limerick Bennett's History of Bandon British Sources for Irish History, 1485-1641 Burke's General Armory Burke's Family Records (various) Calendar Documents of Ireland Calendar of Archbishop Alen's Register Calendar of Christ Church, Dublin, Deeds Calendar of Inquisitions, Co. Dublin Calendar of the Liber Niger and Liber Albus, Proc. RIA 27 Calendars of Carew Mss. Calendars of Inquisitions Post Mortem and other Analogous Documents Calendars of Justiciary Rolls, Ireland Calendars of Ormond Deeds Calendars of Papal Registers and Letters Calendars of State Papers, Ireland Cartulary of St. Mary's Abbey, Dublin Cartulary of St. Thomas' Abbey, Dublin Census of 1659 Chancery Inquisitions, Leinster Charters of Duiske Priory, Proc. RIA 35 Civil Survey, volumes for Kildare (8) and Limerick (6) Commentarius Rinnucinnianus Crown Survey of 1542 and Kildare Rental D'alton's King James' Irish Army List Dignitatus Decani of St. Patrick's Cathedral, Dublin Dowdall Deeds Extents of Irish Monastic Possessions, 1542 FitzGerald and McGregor's History of Limerick Frost's Toponomy and History of Co. Clare Gilbert's Contemporary History of Affairs in Ireland, 1641-1652 Gilbert's History of the Confederate War in Ireland Gormanston Register Hayes' Mss. Sources for the History of Irish Civilisation Hore's History of Wexford Index to Dublin Grants and Wills Irish Fiants of the Tudor Sovereigns Irish Genealogist (periodical, 1940-) Journal of the Cork Historical and Archaeological Society (periodical, 1894-) Kings Inns Admission Papers Knights' Fees in Counties Wexford, Carlow and Kilkenny Landgable Roll of 1665, Dublin City Landowners of Ireland, 1876 Lenihan's History of Limerick Liber Louvainensis McLysaght's Surnames of Ireland O'Kief, Cosh Mange, etc. Parliament and Council in Medieval Ireland Reany's Surnames of Britain Red Book of the Earls of Kildare Register of the Hospital of St. John, Baptist, Dublin Repertorium Viride of 1533 Reportorium Novum 3. Spanish Knights of Irish Origin The Irish Dominicans, 1536-1641 Tresham's Irish Patent Rolls Wadding Papers Wolfes of Forenaghts, Blackhall and Kildare, by R.T. Wolfe Worthies of Thomond Manuscripts National Archives, Dublin: RC 4/8 RC 7/1, 7/3, 7/12 RC 8/4 RC 9/6, 9/12 Fergusson Mss. Prerogative Grant Book, 1749 Index to Limerick Wills Mss. M 2550 Genealogical Office: 159, 165, 189-193 National Library: 113-118, 761 Index, Griffith's Valuation Public Record Office of Northern Ireland: 3078/1