Blink was a paradox/bad science or badly explained, but I am banking on the former since RTD is not as good as Steven Moffat. Yes, time-streams do not run linearly, but what happened in Blink could not conceivably have happened unless Sally, figured out on her own the first time, which I doubt that she did.
Regarding the Pandorica, easy explanation is that it was not an impenetrable prison after all, and that the Doctor escaped somehow and acquired a vortex manipulator since he no longer had access to the TARDIS.
The River Song arc is not paradoxical at all.
Let's say that Doctor A (which is the very first instance of the Doctor) reached the Field of Trenzalore and River A (First instance of River was not stolen from The Doctor's timeline). The Silence then go back to steal River B (Younger instance of River) in order to prevent The Doctor from reaching that point. River B grows up to attempt to kill Doctor B and uses up all her regeneration energy to save him, and the Doctor does not find out about his death since it has not happened yet. Eventually, River B ages some more, and is caught by Kovarian and sent to kill Doctor B (An instance of the Doctor after Doctor A), who is the first Doctor and ONLY instance of the Doctor dying at Lake Silencio. River B goes back in time to the Donna era with Doctor C and dies (First time that the Doctor is called to the Library since River is the one who beckons for him to come). The second instance of The Silence intervening results in a River C that uses up all of her regeneration energy to save Doctor C (older instance of the doctor), who finds out that he dies at Lake Silencio. The Teselecta dies in Doctor C's place for all of future instances of this scenario when River C kills it after finding out that the Doctor has no intention of dying, and River D and Doctor D (delayed invite for The Doctor) are invited to this event. River C does not suggest to Amy that she already knew that it would happen, just that she knew that the Doctor did not die. Eventually River C calls Doctor E to the library and is saved this time because Doctor D gave her his screwdriver in anticipation of her death. After it happens once again with River E and Doctor E being invited to the event, River D tells Amy that she already knew that the Doctor D wouldn't die as she had been invited to the event when she had been younger. I believe that the Pandorica occurred as a result of The Silence eventually finding out about Doctor D (and future instances) surviving to reach Trenzalore, resulting in the second Big Bang first occurring in Doctor E's timeline. Yes, I do believe that many extra points in time were created for future instances of The Doctor as they could not have feasibly occurred in previous scenarios where the timeline was being fixed so that The Doctor could reach Trenzalore.