Does your son sing? It's common for stutterers to be able to sing just fine. I've had a very hard time with "yes" once or twice in my life. As a kid, after discovering that I could sing even when I couldn't talk, I struck upon the idea of imagining short phrases or single words as things I was singing rather than speaking, especially when I could imagine, for example of a song where the word "yes" was used. A "yes" held slightly longer than normal may or may not strike a listener as slightly odd, but if it's the only way to get it out smoothly, it can be as lovely as any song, short and sweet.