I was going to suggest what longnose did, elevating the refugium. Eliminates the issue of potentially cracking the glass if one tank shifts or if the tanks aren't aligned properly (might not happen immediately). If you need to do maintenance, or when you graduate and move or just move off campus, it will be easier to manage the tanks as you will not have to separate the plumbing to do so. Experimentation and maintenance will be easier.
I have drilled smaller tanks many times successfully. Plenty of water to flush the grit and patience are key. But shifting plumbing and misaligned plumbing will crack those tanks in a hurry.
I would personally raise the refugium a few inches and have the drain lines go to the primary sump with a valve and a teed off section that diverts a portion of the flow to the refugium. I am of the camp that believes the refugium should not recieve high flow, should recieve unfiltered water (ditritus and suspended particles to feed organisms that in turn help feed the tank), and should drain into the return pump section where organisms don't have the posibility of being sucked up into the skimmer or other filtration devices. I also prefer a Jaubet, or plenum, system to help control nutrients. Just dumping a bunch of sand in there doesn't quite accomplish the purpose of a deep sand bed. I am also starting to experiment with miracle mud, splitting my sump into half Jaubert method, half miracle mud refugium.
It is more flow through the refugium than I would like, but I don't have the space to do something different at the moment.
Ideally I would set the refugium higher than the aquarium and have that drain directly into the display, but that is a different matter than what you are trying to accomplish.