I carefully cut the holes for the various parts, for instance, intake air, exhaust air, and the places where the cables connect to the motherboard and cards. I used three different kinds of large-hole-drilling tools, as well as a lot of Dremel work.

Note that the protective adhesive plastic is still on the plexiglass in these pictures.

In the final design, the idea is to create a positive-pressure system where the 120mm fans blow cool air into the case from the front, and exhaust all hot air through holes in the back of the case. So all airflow is one direction. Many of the holes on the back of the case are only there for the purpose of exhaust air.