Here's a quick update:

I've taken the previous model apart, and started anew. The previous cage was not nearly as stable as I wanted it to be. This one will be better. As you can see, The MB has been rotated 90 degrees to fit the 120mm fan. This, as well as the area between the GPU and cage wall, will hopefully make room for all the cables that are connected to the PSU.

The GPU has to be supported, and that is what the black and grey column does. The little red brick has a 1x1 round red "brake" brick to hold the GPU firmly in place and 90 deg. to the MB. I've used arches to go up in height, and a cage has been constructed around the CPU to elevate the PSU and secure it, where it will suck the air out of the CPU cooler. The HDD is laid flat upside down in between the CPU and the 120mm fan to keep cool. I'll use rubber "feet" from the Mindstorms set to secure the HDD and minimize noise from vibration.

This is what the CPU cage looks like. I've removed the HDD to fit the IDE cable. I had to remove the slave connector pins on the IDE cable to make it more flexible. It now bends and runs below the GPU. The cage is cleverly connected to the main LEGO structure and forms the "bed" for the HDD along with the beams used to secure the 120mm fan.

More updates to follow tomorrow.