Some helpful tools in examining Bach's Saint John Passion.
Pamela Dellal's translation of the libretto for Bach's Passion according to Saint John is a great place to begin to study the text the great Cantor sets.
John & Synoptics
John's Passion account differs from the Synoptics -- Matthew, Mark and Luke -- in substantial ways. When you try to "harmonize them", this is make them work as one unit, the result is not only bizarre, but particularly harmful when it comes to "the Jews." Looking at this outline may help you understand how John stands as a distinct entity from the other Gospels of the New Testament.