I have no problem whatsoever in him aging over 1,000 years from Eccleston to Capaldi.

What I do have a problem with is that from McCoy to Eccleston he aged MINUS 53 years!

I'm sure it was said the War Doctor, between McGann and Eccleston, lasted a few hundred years during the Time War.

He lied about his age.

Wouldn't you if started out looking like McCoy and ended up looking like McGann - that's a hell of a result.

Yes, I'm aware of that, but I think you've missed my point.

Eccleston told Rose that he was 900 years old, yet McCoy mentioned in his first story that he was 953. Hence MINUS 53.

Ohhh, my bad, I misread it. :P

Serious answer - it's never been established how the Doctor measures his age.

What is a year - a year on Earth - or Gallifrey - something else?

How do you measure "a year" if you're not even near a planet that HAS a rotation?

What about changes made to timelines?

What about entropy and it's relationship to distance from the centre of the universe?

What about the effects of travelling faster than light?

Basically - the Doctor's "age" is no more able to be accurately interpreted than "star dates" were in classic "Star Trek".

As far as we know, since the Doctor's taken to picking up his companions for regular trips nowadays, the Doctor we see in one story may be an earlier one than in the previous adventure, from the companion's point of view. If that makes sense.

It does but you're missing the fact that Johnny was talking about him losing 53 years AFTER two regenerations - your point misses the changed appearance

In the classic era he could have been using Gallifreyan years then once that was gone he started to use Earth years

If that theory is correct I know The War Doctor used Earth years to but as he had a mind link with the other Doctors (It wasn't shown but past multi Doctor stories shows that does happen when 2 or more Doctors meet up) he could have used Earth years for Clara's benefit

The age thing doesn't bother me,I thought it was established that the Doctor is always vague about his age and wasn't even sure himself.
The amount of time the War Doctor was supposed to be around doesn't seem right though as it seemed to be the last days of the War when McGann changed

I'm with you - never bothered me beyond knowing that he's very old - but I get that he should never get younger.

Yup. I always thought RTD dropped a bollock with the age issue.