The power supply is good for about 2.5-3A at least continuously on both the 5 and 3.3v rails. If it's overloaded it should simply shut down. Certainly a short will make it die instantly with no damage.

The whole thing is also fused at a level which should prevent damage with resettable polyfuses. It's actually fairly difficult to damage the empeg psu, it's deliberately overdesigned to be very robust. If smoke came out after several hours operation, it implies something has slowly overheated. This seems to me to be unlikely to be the PSU, as under a constant load it would come up to it's maximum temperature quite fast, no more than 5 minutes or so.

The memory board presents a fair extra load to the supply, but well within usable limits. The button LEDs don't take more than a few 10s of milliamps at worst, and I can't imagine that the digital out board takes more than perhaps 100mA at the most.

The fan is a possibility, as if it jams (as Rob S suggested), it can end up drawing a horrendous amount of power. I have had one of those little brushless jobs get so hot it melted the solder holding it's innards in place, so them immediately became outards.

I would suggest that the first thing to do is measure for shorts between the dc in line and case ground, then between the 5v, 3.3v, and internal dc in points, to ground. With the fan both connected and disconnected.

pca