The Second Doctor said he was 450 years old. He also said that barring accidents Time Lords could live forever. The Third Doctor said he had been a scientist for "thousands of years". The Fourth Doctor said he was only 749, not 750. The Tenth Doctor said he was 903, then we saw when he passed 1000.
The "Twelve regenerations" thing was first mentioned when they brought back The Master after Roger Delgado died. This was in The Deadly Assassin, and they said he had used up all twelve of them. I believe that with the Time Lords all gone and The Doctor having become much more powerful, that is now past history. The truth is that he can regenerate for as long as the show is popular. They'll always think of something.
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“Never do anything you can't take back.”
—Rocky Russo
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