From Observations on the role of Greek Philisophical thought in the history of Christian theology, especially as it pertains to John 1:

 

The co-opting of Christian theology by Greek philosophy is a long and complicated history. To really understand it requires much study. One has to be familiar with the Greek philosophers, especially Pythagoras, Plato, Aristotle, and Xenocrates, as well as some important figures in what's called Middle-Platonism - Numenius, and most notably Philo of Alexandria.

 

Additionally, one must be familiar with the writings and teachings of the Church Fathers, as well as the issues and writings concerning the Council of Nicea, the Council of Chalcedon, and so on.

 

Please read the page linked to above if you haven't already. Greek thought has affected almost every aspect of Christianity, both doctrine and practice. It's difficult to know where to begin. The fundamental issue, I suppose, would be the Nature of God, and its consequent issue, the nature of man.

 

The Nature of God

 

God's Place in Time and Eternity

 

​The Nature of Man: Is the Human Soul Inherently Immortal?

 

The Structure and Function of the Church