How about removing the CPU cooler?

The CPU cooler is made out of aluminium, not the absolute best material to disipate heat, but possibly good enough for this system:

There are four screws that fasten the cooler to the board:

While at the bottom, there is the copper base:

Let's start our installation, CPU and memory are in their places:

HDD is placed in the storage bay:

Optical storage drive also:

The pre- attached cable clamps on the side of the PSU keep cables together and tidy:

Two more HDDs are installed in the top racks, notice the installed cables

Finally, we need to install a VGA card. There is a 6pin PCI-E power cable if required. For our tests, we selected a passive cooling solution, the MSI 7600GT.

Which however is too big to fit in the case, and you cannot close the box. Shuttle should have taken this into consideration, since most passive cooling solutions for VGA cards have such big copper heatsink: