Caponizing can be done on a duck, but take him to a vet since he's your only one(also caponization is best done on young birds). We've caponized several of our cockerels with good success, but it is super tricky and not for the faint of heart.
Sounds like you're on the right path. We have our tom turkey seperate from our chickens and seperate from our ducks, etc.
