> First it re-scans the entire
> site again drastically reducing the time available to
> download new stuff before it shuts down again.

Are you using "Continue an interrupted mirror" ? 
(NOT "Update an existing mirror")
It should be quite fast (and should not trigger any data 
transfer)

> For
> some reason this is not repected for 404 errors and it 
will
> overwrite a perfectly downloaded page with a 404 error 
page
> instead of leaving the good download as it is.

Err, err, this shouldn't be. Try to activate "No error 
page" too, but this is a definitively weird behaviour.