Nate -- The following resources, while not comprehensive histories of theological education, may nevertheless be of some interest:

Robert W. Henderson, The Teaching Office in the Reformed Tradition: A History of the Doctoral Ministry (1962)
William A. McComish, Epigones: A Study of the Theology of the Genevan Academy at the Time of the Synod of Dort, With Special Reference to Giovanni Diodati (1989)
Walter Steuart, Collections and Observations Concerning the Worship, Discipline, and Government of the Church of Scotland (1709, this edition 1770)
Matthew Poole, A Model for the Maintaining of Students . . . at the University . . . in order to the Ministry (1658, to be republished by The Matthew Poole Project)

Older threads:

Education at the time of the Reformation - Bibliography
Office of Doctor

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Andrew Myers
Husband of Jessica, Father of Jackson, Katie and Samuel
Member, Presbyterian Reformed Church of Northern Virginia
Warrenton, VA USA
Editor, The Matthew Poole Project

"Let your Morning Thoughts, and your last Evening Thoughts, be what shall become of you to all Eternity." -- Matthew Poole