what JohnRob said, but:
get a PC board drill set. twist them by hand to mark the hole centers. a second use: when you have to replace a header, don't waste time and risk damage with heat, solder suckers and solder wick. just use a PC board drill, twisted by hand, to extract the solder from the hole.
control a Dremel: it is not a scalpel, don't hold it like one. dominant hand on the body of the dremel holding the tool vertically. forearm resting on the table. non dominant hand on the work piece, at a right angle. non dominant hand acts like an X-Y controller, dominant hand is the Z axis control. if you move more than your fingertips you're holding it wrong.
when I make templates for modules I put a + in the mounting holes as a center marker. You should be able to drop the module on the page and see 4 +'es and a thin dotted line inside the hole. I use Libre Office Draw, open source, free, pre installed on Linux.
my preferred technique:
- mark, drill, tap.
- put a 4-40 or metric screw in the tapped hole as required.
- put a nylon nut on that for spacing the solder pads away from the plastic.
- nylon couplers, also known as standoffs, to hold the module. these are much easier to install than scrawny little nuts, if you have kielbasa fingers.
you need nerves to make a large project box from clear plexiglass. mistakes glare like neon.
If I had a 3D printer I would try this: flat panels, thinned at hinge points. One edge of each panel round, the opposite edge C shaped. Mount and wire modules and controller laid flat, bend it into box shape, snap round edges into the C shapes, and voila: a compact box that a guy with hands by Hormel can work in.
it would be a fine and wonderful thing if some Arduino forum would set up a place where fussy perfectionists could post module templates in .odg format. one guy who does it well does the work, the whole community benefits.