Anyhow, I found a way to clean out the holes in the DivaCup without enlarging them, but still getting them really clean. Presenting:
It's designed to get into spaces with tricky dental work, like bridges. So it has a small end that can be easily threaded through the DivaCup holes, and after you pull that through there's a puffy part that will clean the holes thoroughly.
The downsides are:
1.) It's expensive for dental floss
2.) You have to throw it away. It doesn't create a whole lot of trash, but it might deter some people.
Regardless, I've made cleaning the holes with SuperFloss part of my DivaCup cleaning routine. It's a little odd, but I hope this helps someone out!