Does the son's inability to sit for long with his father, or to confide in him, or to feel completely at ease with him—despite his promptness in fulfilling his father's requests and avoiding his displeasure—count as disobedience for which God will hold him accountable, especially since this feeling is beyond his control and stems from the father's aloofness towards him alone while showing affection to others?

You have forgiven your father and prayed for his forgiveness. Mere heartfelt feelings towards him are not blameworthy, because a person has no choice over them, and there is no obligation except within one's capacity, as Allah Almighty says: "Allah does not burden a soul beyond its capacity." Disobedience (uquq) occurs through a statement or action from the child that harms the parent. There are many forms of righteousness (birr), including: supplication (dua), financial support, and checking on their well-being.