I saw a picture from the parts when Franky visits the Future Kingdom (I haven't reached those parts of the series actually, so I don't know the context), with his metallic skull, chest, and other body parts exposed, as lacking skin coverage.
It was also visible on the way to Enies Lobby that his hip can be attached in length (reversed Centaur ability), but in the post-EL episodes people were disgusted by him running around naked, meaning he's likely not different from a typical male in this aspect.
Considering these and a lot other moments (such as the cola fridge replacing his stomach), it's pretty hard and almost impossible to determine how much of him remained human.
Is there anything we can know for sure? What I could judge so far is that his arms are entirely replaced (which is obvious seeing his post-TS appearance), but I was surprised that even his skull isn't original anymore.