Crazy idea?
This may be a crazy idea and one that I have not tried but it's based on a vague memory of a setting in iTunes that lets you set the volume on individual songs.
Find a song that is the length of your pause. I realize that may be tough since a pause should only last a few seconds but maybe you can "compose" one?
Then, set the song's volume to none or low, and then create a playlist of your music and put the low volume song in places where you want the pause.