It is at this point that it is critical to make sure the drive is level and exactly where we want it.
I was able to check for squareness and use a level before proceeding to the next step.
With the drive ready, I can start to drill holes. Unfortunately with the problems inherent with photographing something transparent, tinted, and reflective none of the pictures of before drilling were usable. Essentially what I did was sight through the Plexiglas to the holes on the drive and mark their location with a marker. Using these as a guide, I then removed the drive and proceeded to drill.
As you may or may not be able to tell, I drilled holes for the screws and then used a larger bit to countersink them. This is to allow the screws to sit flush with the case when the drive is mounted.
It was at this point where I discovered my initial plan for fans was not going to work. I was going to have to drill out a 80mm fan hole in the plexi without the benefit of a laser. After figuring out where I wanted the fan, I found the center of that point and used the same drill bit to drill a pilot hole.