Does preferring those who raised the questioner over her biological parents constitute disobedience, and is this preference the cause of her academic distress?

Difficulty in studies or marriage is not necessarily a punishment for a specific sin. However, the fundamental principle is that a servant should blame themselves, repent, and seek forgiveness when facing difficulties or a lack of success, as Allah Almighty states in the Hadith (definition) Qudsi: "So whoever finds good, let him praise Allah, and whoever finds other than that, let him blame no one but himself." If there has been a shortcoming in one's duty towards parents, then repentance is due, and one must honor them and treat them with kindness, even if they have been abusive or distant.