Is it "Twins: A Different Life"? I read it and this sounds like that.
Harry is banished to the Dursleys. Merlin steps in and transports Harry back to the time of the founders. Yes this is cliche but really there are only so many ideas but the author knows this and does not spend a lot of time there. Instead we meet a confident, cunning, ambitious founders heir who is determined to teach his birth parents and Dumbledore a lesson.
From Chapter 3:
"In your defence, I am a fire elemental and sending fire back at me was not the best of ideas." Harry pointed out with a shrug, Salazar raised an eyebrow at him and Harry smirked. "Ok, so I was completely amazing, I know, but I was trying to make him feel better." Both Godric and Salazar rolled their eyes and the three of them began fixing up the damaged room.
From Chapter 12:
"I have an animagus form of a phoenix, a black one actually, the reason I was out so long was because the healing abilities only work in my conscious mind and I had to get back in to it." He told them and then left with Draco leaving them more confused than ever, they looked at each other in shock.