Searching for Consistency

Yesterday was Yom Kippur - the Jewish Day of Atonement. This is never an easy time for me...as I am sure is the case with many of my co-religionists. This had nothing to do with the physicality of the fast and everything to do with the self-reflection that the day requires. I felt as though I was spinning wheels in my mind...debating issues of good and evil, faith and reason without reaching a conclusion one way or another. I have my core metaphysical beliefs that I express on this site but my challenge... and it still remains asuch....is how can I meld these in a world where science is so critical. What must give and what can stay? How can I remain consistent? True to G-d but loyal to rationality. Where do my assumptions begin?