I am trying to do the following:

Hello Bob

setTimeout (5000); // i.e. pause for 5000ms

Bob? Are you there?

How do I do this?

Did you ever figure it out, dennmans?

You could do it like this:

[[Start]]:
    setTimeout(function () {
        squiffy.story.go("next");
    }, 5000);

Hello Bob!

[[next]]:
Bob, are you there??