I have a Non-Jewish father and I want to know how I should be called to the Torah and what name should be written on my ketubah. Should i go with Binyamin Tsadik Ben Avraham or with Binyamin Tsadik Ben Chayim (My mother’s father) because Rashi says in relation to Yitero’s names that the father’s father is like the father?

Even though you are not a Ger, you should still be named "Ben Avraham" since Avraham is the father of the nation and you do not have a Jewish father. Rabbi Chaim Kats.