Which religious groups were strongest in Ireland and the Scottish Highlands under Stuart rule?
Beginning with the reign of James VI of Scotland (also, James I of England) (1567) and ending with Queen Anne's reign (1707), which comprises the reign of the Stuarts, with some minor exceptions, the predominant religion in the Scottish Highlands was a form of Protestantism. The dominant religion of Ireland (not in what is now known as Northern Ireland) during this period was Catholic and, in the area known as Northern Ireland beginning in the 17thC, Scottish Protestantism was the dominant religion. As we now know, the influx of Protestants into northern Ireland in the 1600s set up a religious, cultural, and economic conflict that has only recently subsided into a truce.
With few exceptions, the Stuart monarchs were anti-Catholic, with the exception of James II, who converted to Catholicism and eventually left England for France where he died in 1701. In the parts of Scotland closest to England, there was a small minority of Catholics, for the most part, from the landed gentry, and in the Highlands, several large clans--the MacDonalds and Ogilveys--were Catholic, but these clans comprised a minority given the number of Protestant clans. The Highland clans, especially the Catholic clans, participated in the Jacobite Rebellions of 1715 and 1745, attempts to restore Catholic Stuart monarchs to the Scottish throne. In general, Catholics, no matter where they were in Scotland, had been persecuted by the Stuart Dynasty (again, with minor exceptions), and most Scots who wanted to thrive economically and socially in the 17thC. and early 18thC. found their way to what in Scotland is called "the Kirk," a very strict form of Protestantism (essentially, Presbyterianism).
Ireland, as I noted above, was essentially a Catholic country--and highly persecuted by the English because of its adherence to Catholicism--with the exception of a small part of northern Ireland that had been colonized by Scottish immigrants in the early 17thC. There, the Catholic natives were persecuted mercilessly by the Protestant Scottish immigrant minority, with the help of the English, and this situation sparked a hatred between the two groups that still exists (but is less violent in recent years).