Events between 1640 and 1660 did confirm the dominance of the English state over the three kingdoms of the British Isles, both by means of political and military involvement. The state went through periods of being dominant as well as being absent from dominance during this period in time. Absent due to the English Civil war, which for a time allowed Scotland to have influence over parliament and for the Catholic Irish to rebel in Ireland. These events were extinguished with the eventual execution of King Charles I, and the formation of the Republican parliament in 1649. The new parliament used the New Model Army to claw back its dominance with invasions into Scotland and Ireland. The new parliament then was able to dominate Scotland and Ireland politically through the eventual Commonwealth government. .
Events between 1640 and 1660 (it could be argued) wouldn't have happened if it wasn't for Charles I tampering of religion. His role before 1640 was important to the events played within the period. Each of the three wars (it could be argued) came from his political failings. His desire to reform religion in each of the three protestant churches, brought dislike for him as monarch. He not only alienated his own parliament, but the parliaments of both Scotland and Ireland. People's beliefs and ideologies is a subject Charles I should have stayed away from in his tenure as head of state. In theory I can see some of his intentions for religion were good. Why shouldn't England, Scotland and Ireland share the same Book of Common Prayer for instance? They each shared the same king after all. Charles took bad advice from people he trusted (William Laud). His actions would ultimately lead to his eventual beheading by parliament, which brought a closure to the English civil war (Anne Laurence and Rachel C. Gibbons, 2011, p. 21to 62).
During the Civil war (1642-1649) parliament suffered it greatest military failures in 1643, at the hands of Charles I and his supporters.