The cat and mouse game with Graham and Hannibal just started and it's going to be incredible. I think Will 'got' the cannibal part of the Ripper when Hannibal started talking about turning anatomy into food. I don't think he connected Hannibal completely but from the way he was watching him in the ambulance and with how he acted at Hannibal's I have to think his spidey senses are tingling.
In the movie Red Dragon, Graham tells Hannibal that he suspected something was off with him before he found the recipe book.
They already used up the final clue that caused Graham to realize Lecter was the killer, and the FBI trainee lost her life over it. Graham OTOH just got gutted for his trouble.