Harry Potter/Sekainohate de Aimashou X-over
Here's the manga address to read the manga if you never have before.
www. mangatown manga/sekainohate_de_aimashou/
Hogwarts starts when the students are 14 years old before September 1st so first years are 14 when they start and when they leave as 7th years they are 20-21 years old. Two years before they start school when they are twelve they are told about magic. Those two years are then spent learning the basic rules about the English wizarding world (and others if they are interested). Harry learns about the wiz world at twelve and starts to prepare to go to school.
He got special trunks (Radaslab's trunks from Not Normal are the best ones I've read of so far, just add or change things as you want). HP is a genius with an I.Q, of 350 by 11yrs old and climbing so by the time he's 12 he's in his final year of high school.
Starts the year before Harry goes to Hogwarts when he's 13 and he saves the Prince and is turned into a girl. He saves the Prince just like in the manga and turned into a girl and the Prince is three years older than her. The whole world non-magical and magical (not counting the English wizarding world (i.e. purebloods and half-bloods raised ONLY in the magical world) because they are idiots and not only that but though out the story they keep pissing of the Prince) know about Emilio (the Prince) and aliens/magic. Female HP looks like her mother with black hair that in light shows some red, and her father's nose and lips. HP never needed glasses.
HP doesn't have a BIG problem with what's happened but is pissed because it was done without his/her permission. And NO Dudley does NOT act like Yuuji. You can create someone that acts like him if you want. Dursleys' are fine with the Prince because they want money but what they don't know is that once they are married they get nothing. The volumes/chapters can be spaced out over all the years with Voldemort dying completely at the end of 4th year at the earliest or one year after 7th at the latest. They marry by the time HP is 22 years old.
Years 1-4 happen the same with a few changes.
Yr. 1- she always wears a mokeskin pouch around her neck that is spelled to not let anyone other than herself and those she chooses of her own free will to see let alone put things in. If something is in contact with her if she thinks about it, she can cause it to appear in the pouch. She now owns the stone.
Yr. 2- The basilisk does the something but in the end that Ginny stays asleep until a week after she's saved, the snake is still alive and it now only follows her and the Prince because he can also talk to snakes
Yr. 3- The Prince gets Sirius free by threatening the WW with total destruction if they don't give him a REAL trial.
Yr. 4- She is still called to compete but is able to choose someone else to do the tasks for her because of a rule (ex. last of a line the can produce kids but has not can chose their own champion to compete for them, the can be anyone of any species). She's kidnapped during the third task and things follow as the book. You can change the tasks if you want.
Year 5 is when this really starts with manga volume 3 around chapter 34.
The story goes, however, you want afterward.