I've wondered about this too. Perhaps the foci being fully charged triggered an alarm...like the button popping out of a turkey.
Or perhaps while wandering the fade he was actually fully aware of the passage of time and knew when to wake himself up. Since according to Dalish legend elders sometimes awoke from Uthenera and shared the knowledge they acquired in the Fade, they must have known how to wake themselves up.
So then...if he was acutely aware, then he spent over a millennia walking the Fade? I mean good for him and all but, at what point does he decide, oh I should probably try to the fix the world now after every one has screwed it over a couple of times.
And if he wasn't aware? Well I find it very difficult to believe that he just woke up from a sleep that long. It just seems too convenient. Why then? Sure it has to happen some time, but why not earlier? Or another thousand years later?
I think someone/something interfered with his sleep and woke him up purposefully.
Now I'm thinking if Mythal had something to do with it.
Now I'm thinking about if she's manipulating all these events to get her revenge!!!
Sorry, tin foil brain engaged for a second.