I was born to an assimilated Jewish mother and a non Jewish father, and I was raised secular except for afternoon Hebrew school in a US conservative movement synagogue. Now that I am Ba’al Tshuva, do I automatically adhere to my great-great grandparents Ashkenazi Minhagim or am I allowed to "pick and choose" Minhagim based on my own desire? Also, as there is variability within some Ashkenaz Minhagim, which would I choose? I’m not certain exactly where my family came from in the 19th Century.

You should pick an Ashkenazi tradition with which you feel most comfortable and try to be consistent in observing the customs of that tradition.