Stones

CSI scene: CSI team are watching a security video taken of a big tough looking guy gambling in a casino. They notice that a little guy standing next to him keeps ripping off his chips under his nose. Eventually the big guy notices and threatens to flatten the little guy.

Jorja Fox says, "This guy's got stones taking on a big guy like that".

Obviously this is an equivalent of 'he's got guts or balls to take on a guy like that'. But why 'stones'? Is this a metaphor for testicles?

Yes I believe so, cf "rocks". It may be an abbreviation/corruption of "balls of stone/like stones", which itself brings up the very similar expression "balls of steel".