Have you redirected the two sites that were causing duplicate links using a 301 redirect (& told Google about the change of address through GWT?

Links can take quite a while to be removed from GWT, but it does happen..eventually!

The fact that the ads are showing and not your pages on your domain sounds like you either have very low domain authority, and the domain authority of the ad websites is higher and therefore ranking above you, or you still have an issue/algo penalty from your duplicate content (or something else).

How long ago did you remove the duplicate content?