The Cromwellian Settlement of Tipperary by J.G.Simms can be read here at the Tipperary Library site. It is very interesting and informative. There are many out of print issues online here as well.
“The result of the Cromwellian settlement was that by 1660 at the end of the Commonwealth regime virtually all Tipperary was in the possession of Protestants” and according to Simms “the foundations of much later strife were laid in the Cromwellian settlement.”
There are quite a lot of out of print Tipperary Historical Journal articles which can be read online free through the Tipperary Library Local Studies site.