What is your advice for atoning for my undutifulness towards my father, whom I never saw or honored during his lifetime, given my intense regret over this?

The mere separation of parents does not permit neglecting the rights of either of them. Obeying one parent in boycotting the other is not permissible. Your boycott and abandonment of your father, despite your ability to reach him and fulfill your duty towards him, is considered disobedience to parents (Uquq al-Walidayn), and it is one of the greatest major sins. You must repent to Allah, increase in good deeds, and make up for what you have missed in honoring your father by supplicating for him, giving charity on his behalf, maintaining kinship ties, and honoring his friends. You should also get to know your relatives from your father's side to maintain ties with them, as Islamic law encourages knowing one's lineage to uphold kinship.