Of course I post this discussion and figure out an answer less than a minute later! Here's how I did it:
1. Create a plane that intersects all the small diameter extrusions
2. Create a section view (modeling) and select the plane, leaving only the small diameter extrusions
3. Select them all with a green box (lower right to upper left)
4. Do an intersection curve extraction
could you not create a 2D on the flat face, turn on your edge filter, fence select all the holes and then do a convert entities?