I grew up in a home with parents who, while proudly Jewish, were non-observant. I am now a Baal Teshuvah as is my wife (same kind of background), and as I have learnt I have picked up quite a few discrepancies in the customs I was taught growing up. The customs my father keep seem to be a mix of Sephardi, Ashkenazi and Yekke. I have no idea where he got such a conglomeration since all eight of my great grandparents are from Lithuania (although three of my grandparents were born in South Africa). My question is- do I follow what my father does or move to the Ashkenazi Litvak customs that my great grandparents would have utilised?

Since the conglomeration of customs of your father does not represent the custom of a specific community, they are not binding on you and probably would cause confusion to you and your children. If you are in a community where straight "Litvish" is "In", that would be fine, but if your community is mixed you have a bit more leeway if there are specific customs of your father you wish to maintain. At any rate, consult your LOR about specifics.