1) During "The Deathly Hallows", the Bathilda/Nagini attack is successful, and Harry is hopelessly poisoned beyond Hermione's ability to heal him (Dittany? Bah!). Headmaster Snape must use the anti-venin he concocted for Arthur Weasley on Harry, in secret. Bonus: What happens when one horcrux attacks another??? Harry is deeply affected.
2) Aunt Marge: "Do they use the cane at St. Brutus's, boy??" Glib, lying Harry: "Oh, yeah. I've been beaten loads of times." That fib comes back to haunt him when he crosses Snape one time too many.
3) Adult Harry is the lonely, disaffected, disillusioned, mistrustful man he ought to have been in canon, going by his childhood neglect and treatment by the Wizarding World. He needs a Daddy, who needs a good boy to love to heal himself at the same time.