Is it permissible for a woman to perform ghusl (ritual bathing), prayer, and have marital relations after the cessation of menstrual bleeding but with the persistence of dark discharge that appears once or twice a day?

The dark discharges you described are "kudrah" (a brownish discharge). This is considered menstruation if it occurs within the customary period or if it is connected to blood, based on the statement of Aisha (may Allah be pleased with her): "until you see the white discharge (al-Qassah al-Bayda’)." If it is connected to menstruation, then ritual bathing (ghusl (definition)) is not sufficient, prayer is not valid, and it is not permissible for your husband to have intercourse with you. However, he may enjoy anything below the private parts. But if a woman sees this discharge after becoming pure (after ghusl from menstruation), she should not pay attention to it.