Step 3: Put in the Motherboard
Now instead of placing the mother board into the case and screwing it to the case itself, lets make a platform for it out of plexiglass. The primary reason for this is that I wanted the board to "float" and have as much air around the board as possible. So get out that plexiglass, measure the size of the motherboard, and cut out a piece of plexi that will cover the entire size of the motherboard's bottom. I used a radial arm saw to cut this out and was shocked that it didn't shatter it and cut it fairly well, just keep on the protective film on the plexi until all modifications to it are complete.
Now simply lay the board on top of the plexi, and using a marker, simply mark the holes where the motherboard will be bolted into it. Use your drill and make the mounting holes in the plexiglass.
Ok, now remember those nylon spacers from the material list? These are what separate the motherboard from the plexiglass to create that air flow for all around the board. So, lets mount the board to the plexi and lay it in place. This gives us an idea of where the motherboard will be in relation to the back panel that we have to cut out.