I spent way too long on this quest because most of my time was spent looking up guides. Hopefully it wasn't just me, but I had a lot of difficulty with this quest, and it's embarrassing how unhelpful the guides online are (both the official guide and various other ones around the internet). So, I thought I'd try to offer some tips to any other players to save them the headache:

1. First off, you don't need beehive bombs. Grapeshot bombs will do fine.

2. Two breaches are close to the first two bodies you find (the bodies that contain keys and Balin's Journal). You may see a faint light shining against the hole. Get close enough so that the prompt to place the bomb shows up.

3. The last breach is at the southernmost part of the room where the dwarven immortelle is. I missed this because the Bullvore blocked my path and I couldn't clearly scope out the room. Just take time to really run around after that fight so you find everything you need.

I hope this helped, but hey, if I'm wrong, let me know and I'll fix it. This is based on my first time playing the Enhanced Edition, so I don't know if there are differences between versions or story paths.