Hermione would surely be one. She's smart and would be great at helping with the academic side of building a school, like creating the curriculum.
Hermione could be a main character. She would use her intelligence and vast knowledge of magic to help Harry plan and build the city. Her skills in research and spell - casting would be invaluable.
Hermione would be a great help. Her vast knowledge of magic and books could provide the necessary information for building the planet, like the right spells and magical theories.
Dumbledore might help in a spiritual or advisory way. Even though he's passed away, his wisdom could be passed on through memories or some magical means. Also, Hagrid could be a great help. He could assist in building areas suitable for magical creatures with his love and understanding of them.
His friends Hermione and Ron would most likely be his allies. They have been with him through thick and thin in the original series.
Obviously, the illithid would be a main character. It could be a mysterious and powerful being that Harry encounters. Also, Hermione and Ron might still be important characters. They could be either suspicious of the illithid or try to help Harry understand it better. Dumbledore might also play a role, perhaps guiding Harry in his interactions with this strange new creature.
Snape could also be part of it. He might catch Harry in a rather awkward moment when he's trying to hold it in and give him a hard time. Or, on the other hand, he could surprisingly offer some help in a very Snape - like way.
Hermione would probably be one of the main characters. She's smart and resourceful, so she could help Harry with the administrative side of running the orphanage, like handling finances and paperwork. Ron might also be involved, perhaps teaching the orphans some practical magic skills. And of course, there could be some of the orphans themselves as main characters, like a young girl with a special magical ability that Harry discovers.
Hermione could be one. She might follow Harry to the island to help him out. Another could be Ron, his loyal friend. Or it could be some new characters created specifically for this fanfiction, like a wise old wizard who has been living on the island for centuries.
Maybe Neville could be involved too. He has shown great courage in the original series. In this fanfic, he could be the one who has some prior knowledge about the dragon due to his family's history in the wizarding world. His knowledge could be crucial in helping Harry enter the dragon's territory and deal with whatever lies within.
In addition to the trio, there could be characters like Professor McGonagall. She would surely notice the changes in Harry and might try to guide him. Also, the ghosts of the founders themselves could be considered main characters in a sense. Since Harry is possessed by them, they would have a significant influence on the story, perhaps communicating with Harry or causing events to unfold around him.