I actually used the fly cutter in a variable speed drill and it worked fine. If you go slow, you can get it to work. I tried grinding that sucker with my Dremel tools and the stainless ate them up. Of course, you have to have your mount off to get to it with the flycutter.
BTW, you should mount the box as high on the firewall as you can. If you have a fire in your engine compartment, there's less chance of your box melting (if it's aluminum which it shouldn't be) or less chance of it sucking in smoke if the exiting airflow doesn't flow past the heater box.