To what extent did the rising issues surrounding the Catholic religion during the Renaissance and Scientific Revolution lead to the Reformation? Were other issues more relevant to the Reformation’s beginning, particularly in regards to the conflicts during the High Middle Ages between the Church and the Holy Roman Emperors?

There are many different causes which led to the Reformation and counter-Reformation. Some were theological and ideological and others had to do with issues of power and economics.
On a practical level, the Roman Catholic Church and the Papal States had dual roles of spiritual and temporal power. One of the most important areas of conflict were what were known as "church temporalities," the vast and valuable collections of land, buildings, and other forms of wealth owned by the Church. Under the feudal system, all land in a kingdom was owned (in theory) by the king and given to nobles in return for service. Bishops and abbots, however, controlled vast amounts of land and wealth in countries such as France and England but were appointed by the Pope and loyal to him rather than to a king. These issues were a major factor in the English Reformation and the creation of the Anglican Church, and these issues evolved from conflicts starting as early as the twelfth century. The similar philosophy of Gallicanism affected the relationship between French monarchs and the Pope, but it led to reform rather than a clean break.
Ideological and theological issues were important to Luther, Calvin, and many other reformers, as were issues of corruption in the Church, especially indulgences and simony. The successes of Protestantism had to do with a combination of factors—the political and economic tension between Popes and kings made many local rulers more willing to break from the Church and accept Protestantism as a state religion. The reasons why some countries accepted Protestantism more readily than others varied depending on local circumstances.