I know this is an old thread but I wanted to be on record as saying it is possible to mount a 40x40x10mm fan inside the CD32/SX32. It was positioned between the hard drive (spinning) and memory simm. It is very tight so is held in place by friction and sits on top of an FPGA of some sort so it's in line with the grill! A fan guard with sections of the sides cut out was glued to the bottom of the fan to promote air flow sideways from the CPU/FPU and then blown out of the top grill! Power came from a molex adapter from a spare CD32 psu I had. It keeps it stable unless it is throttled for an extended period of time playing something like Reshoot Proxima III!
I would recommend a IDE2CF card solution to reduce the heat further.
The fan was this model: Noctua NF-A4x10 FLX