I think this is probably bad English (because of that odd initial negative form, followed by the fact that you are actually reading). It's probably more correct to say 'I've been reading for only three hours, not four.'

'Cela ne fait que trois heures que je lis ( que je suis en train de lire ), pas quatre.'

Consequently your rendition is quite correct, though the 'cela fait' usage maybe sounds a bit more of a spoken than written formation.

The more formal translation might be simply

'Je ne lis que depuis trois heures, et non pas quatre.'

I haven't seen Jean for a week.

'Cela fait une semaine que je n'ai pas vu Jean.' Correct spoken usage.

'Je n'ai pas vu Jean depuis une semaine.' More formal written style.

This is quite possibly bollox on my part. But I have noticed that the negative forms of the English Present Perfect always give English speakers a bit of hesitation when speaking French.

Let's see what Jean-Michel says.