but I've been unsuccessful in confirming if the AUX in on the Empeg is converted to digital and back again, or if it's just a straight-through job. In the former case, I suppose it's just a question of locating the AUX-in ADC and bypassing it.

The ADC is built into the DSP, and cannot be bypassed as such for Aux In mode. The DSP does have one of it's digital CD inputs not being used. This would accept an i2s signal, so you'd need some hardware to convert spdif to i2s. In addition, some kernel hacking would be required. And you wouldn't have any visuals for your new 'Aux In' mode. Not that I haven't confirmed that this is feasible physically. That input (and it's associated control line) should currently be grounded. It might not be be possible to break those ground connections - it depends on how they got routed on the pcb. If they got routed under the DSP and via'd to ground then you can forget it. If they got routed away from the DSP on the component layer then it might be possible.

I'm not feeling inclined to crack open my player to check at the moment - I don't think that the demand is there to really make the investment in time, hardware and effort. I suppose that if it is possible that Stu might consider adding an input stage to his soundcard if demand did really exist and it does turn out to be physically possible, but I wouldn't hold out any hope.

For anyone with a copy of the DSP manual who wants to check those lines, you're looking at CD_2. (CD_1 is used for mp3 playback)