Which parts of Franky's body have remained organic?
We know that because Franky couldn't reach his back when he first reconverted himself into a cyborg, that part still remains organic; and according to Senor Pink in chapter 775, Franky's back is still made of flesh after the timeskip.

Robin also managed to squeeze his privates at the end of the post-Enies Lobby arc in an attempt to get him to join, so these parts remained organic as well.

While his head is now partially robotic, as shown with his steel nose and the exposed circuitry from the injuries he suffered from his fight with Senor Pink, it can still bleed, showing that it remains at least partially organic.