Actually, the lyrics are quite ambiguous. Just try to imagine what Tom Waits really wants us to tell what you can do with a Chocolate Jesus.
"I know Jesus loves me, maybe just a little bit more..."
I personally believe that's the hidden irony Mr. Waits wants us to get.
Q: Did the the rooster on Chocolate Jesus get paid? --Tom Waits: He was not paid. He's just transient. But I paid him in one form - he's still alive. And now of course, he's considered a big shot in the barnyard. You can't even approach the guy.
Q: Who plays the rooster on Chocolate Jesus? Tom Waits: --That's a real rooster. Q: Yes, but he was crowing right on cue. Waits: --He was crowing on cue. You know one thing about animals---when you record outside, they'll pretty much wait till you're finished with your phrase. Because no one wants to talk while you're talking, especially a rooster.
LOL artist Cosimo Cavallaro has made a life-size and anatomically correct depiction of Jesus (without loincloth) crucified on an invisible cross sculpted entirely from chocolate: http://www.pacifichighlander.postkiwi.com/?p=617