I had the over-heating CPU problem too. In fact, I already had it before I tried this game, but this one was SO demanding on CPU, that automatically shut down my PC over 10 mins of game (and a hell of stuttering on lower settings). I had to open the case, unmount the CPU fan cooler, apply new thermal paste (mine was almost history) and put the CPU fan cooler back in.
After that, the game played smoothly, and no shut downs anymore. I can't believe that people with beast rigs like yours cannot run the game. My rig is:
CPU intel core i7 930 (2.8 GHz, without OC)
GPU nvidia 750 Ti 2 GB
12 GB DDR3
This game is SO heavy CPU and GPU wise....it puts Watch_Dogs as a light game.