Is my marriage to an orphaned girl with whom I had an illegitimate relationship valid, and what should I do to atone for my sins and gain Allah's pleasure?

Sincere repentance is obligatory for an illicit relationship, and marriage to the woman with whom one committed fornication is not part of that. Repentance is the expiation for this sin, and the parents are not held accountable for the son's crime. Marriage before ensuring the absence of pregnancy (Istibra) – if there is a reason for it – is a matter of scholarly disagreement, and it is valid according to one opinion. Doubt does not affect the validity of the marriage, and it is not permissible to falsely accuse the wife. Do not divorce the wife merely based on doubt, but if what you suspect is proven, discipline her. If she repents, then keep her. If she persists, then separate from her.