As I mentioned, the power supply can be installed with fan facing either down or up. Down will likely keep the power supply temperatures lower, but up could have additional cooling benefits for the hard drive(s). The motherboard and power supply must be installed first, and then the drives mounted to the brackets and the brackets re-installed. The optical bay bracket has slotted holes for the mounting screws that allow some depth adjustment for the drive, so that the face of the drive can be set flush with the front panel.
The 3½" drives are mounted to the bracket through rubber grommets and these special provided screws that maintain the proper spacing so that no metal-on-metal contact is made. Only the 3½" drive mounting holes have the grommets, the 2½" holes go directly through the metal, however these are supplied with the idea of mounting solid state drives which of course do not cause vibration.
Although there is some open space behind the 5¼" drive bay, depending on the CPU socket placement there will likely be enough of an overhang to prevent the use of large CPU coolers. In this case, even an OEM CPU cooler is a bit of a squeeze, and care must be taken to keep wires and cables out of the way of possible contact with fan blades.
Let's wrap things up with some final thoughts and a conclusion.