The events of End of Time part 2 and Day of the Doctor happen simultaneously.
In the timeline of Gallifrey and the time war I believe it happened in this sequence:
End of Time part 1:
Doctor goes to Ood Sphere. (Will explain the 10th Doctor’s timeline a bit later on.) then to Earth, encounter the Master and his plans. The Master turns all the humans into himself.
The closing scene:
NARRATOR: This day was the day upon which the whole of creation would change forever. This was the day the Time Lords returned. For Gallifrey.
TIME LORDS: For Gallifrey!
NARRATOR: For victory!
TIME LORDS: For victory!
NARRATOR: For the end of time itself!
TIME LORDS: For the end of time itself!
I believe that Rasillon attempted the Ultimate Sanction after this.
Day of the Doctor:
(Inside the Citadel.)
ANDROGAR: The High Council is in emergency session. They have plans of their own.
GENERAL: To hell with the High Council. Their plans have already failed.
Gallifrey's still in the line of fire. So, he was there then?
ANDROGAR: He left a message, a written warning for the Daleks. He's a fool.
GENERAL: No, he's a madman.
ANDROGAR: As you can see, sir, all Dalek fleets surrounding the planet now converging on the capital, but the Sky Trenches are holding.
(Boom! The building shakes.)
GENERAL: Where did he go next?
ANDROGAR: What does it matter? This is their biggest ever attack, sir. They're throwing everything at us
TIME LADY: Sir, we have a security breach to the Time Vaults.
GENERAL: The Omega Arsenal, where all the forbidden weapons are locked away.
ANDROGAR: They're not forbidden any more. We've used them all against the Daleks.
GENERAL: No. No we haven't.
I believe the General believes that the High Council has run out of time and he does not know about the prophesy of the Visionary that we will see now. The War Doctor is busy stealing the Moment.
The End of Time Part 2:
Opening scene with High Council.
(Gallifrey is in ruins. Only the Citadel stands inside its protective dome. The man we saw as the Narrator in part one strides across a bridge followed by two acolytes and takes his seat at the head of a table. Six time lords sit, three on each side, whilst a woman is at the far end, scribbling on parchments. The rest of the space is in darkness.)
RASSILON: What news of the Doctor?
CHANCELLOR: Disappeared, my Lord President.
PARTISAN: (a woman) But we know his intention. He still possesses the Moment, and he'll use it to destroy Daleks and Time Lords alike.
CHANCELLOR: The Visionary confirms it.
(The Visionary is the woman at the end of the table. She has henna tattoos on her face and hands.)
VISIONARY: Ending, burning, falling. All of it falling. The black and pitch and screaming fire, so burning.
CHANCELLOR: All of her prophecies say the same. That this is the last day of the Time War. That Gallifrey falls. That we die, today.
VISIONARY: Ending. Ending. Ending. Ending!
PARTISAN: Perhaps it's time. This is only the furthest edge of the Time War. But at its heart, millions die every second, lost in bloodlust and insanity. With time itself resurrecting them, to find new ways of dying over and over again. A travesty of life. Isn't it better to end it, at last?
RASSILON: Thank you for your opinion.
(The Lord President stands and aims his blue metal gauntlet at the Partisan. Energy strikes her, she screams and is atomised.)
RASSILON: I will not die! Do you hear me? A billion years of Time Lord history riding on our backs. I will not let this perish. I will not!
CHANCELLOR: There is, er, there is one part of the prophecy, my Lord.
(The Chancellor brings a paper to the Lord President.)
CHANCELLOR: Forgive me, I'm sorry. It's rather difficult to decipher, but it talks of two survivors beyond the Final Day. Two children of Gallifrey.
RASSILON: Does it name them?
CHANCELLOR: It foresees them locked in their final confrontation, The Enmity of Ages, which would suggest
RASSILON: The Doctor! And the Master.
CHANCELLOR: One word keeps being repeated, my Lord. One constant word. Earth.
VISIONARY: Earth. Earth. Earth. Earth. Earth. Earth.
CHANCELLOR: Planet Earth. Indigenous species, the human race.
(A projection of the planet appears above the table.)
VISIONARY: Earth. Earth. Earth.
RASSILON: Maybe that's where the answer lies. Our salvation. On Earth.
Here we see that the War Doctor stole the moment and is missing. Also the visionary informs them of the prophesy of Earth, The Doctor and the Master.
Rassilon and co goes through the gate bringing Gallifrey with them.
DOCTOR: Listen to me. You can't!
RASSILON: It is a fitting paradox that our salvation comes at the hands of our most infamous child.
Proposed by Lord President Rassilon as the last resort to winning the Last Great Time War, the Ultimate Sanction involved the creation of a paradox so severe that the resulting spatial-temporal rupture would rip the Time Vortex apart.
They tried to do this before and failed, which is why The General thinks the high Council Members have failed. (This is the only part that seems really shaky to me. When the War council meets in Day of the Doctor the War Doctor is busy steeling the Moment, but the General says that the High Council’s plans have already failed. ) I think they might have tried several things before this day.
Moving on in the timeline of Gallifrey and the time war:
Day of the Doctor:
The rest of the events occur and the Doctors save Gallifrey.
THE 10TH DOCTOR’S TIMELINE:
In chronological order and not in episode order:
After Journey’s End 10th leaves Donna with her family and Says goodbye to Rose and his ‘human’ self. He is now left with no companions and either goes through the extra episodes first and then appears in Day of the Doctor or the other way around.
Day of the Doctor:
He finds himself in the 1550’s to 1560’s with Queen Elizabeth I and a Zaigon before the time portal is opened and 11th steps through.
At the end of the Episode we hear that he will forget that he saved Gallifrey.
The End of Time part 1:
The Doctor goes from saving Gallifrey first and then his other adventures alone after Journey’s End or the other way round. He forgets everything we assume.
(The Tardis materialises in the snowy landscape, and the Doctor steps out wearing a stetson and a lei. Ood Sigma is waiting for him.)
DOCTOR: Ah! Now, sorry. There you are. So, where were we? I was summoned, wasn't I? An Ood in the snow, calling to me. Well, I didn't exactly come straight here. Had a bit of fun, you know. Travelled about, did this and that. Got into trouble. You know me. It was brilliant. I saw the Phosphorous Carousel of the Great Magellan Gestadt, saved a planet from the Red Carnivorous Maw, named a galaxy Alison. Got married. That was a mistake. Good Queen Bess. And let me tell you, her nickname is no longer. Ahem. Anyway, what do you want?
So here he mentions that he married queen beth (Queen Elizabeth I), known as the virgin queen.
We know that in Day of the Doctor he married her, but he is supposed to have forgotten it. So my theory is either he just remembers that bit (Which is highly unlikely) or he went back to the moment before the time portal opened in Day of the Doctor.
The Queen was still besotted with him so he probably married her again, because he asked her before the portal opened. He mentions her last in his sentence so I believe his adventures after Journey’s End happened first and then the Day of the Doctor. But it’s all just speculation really and not very relevant.
The whole of End of Time part 1 and 2 happen and he regenerates into the 11th Doctor.
I hope I didn’t bore anyone. Also if you have other suggestions let me know or if you noticed I got something completely wrong.