I guess the first problem to resolve is the hardware interface?
The LEDs on the front are driven by port pins, so they could be used OK.
Question is how to connect an infra red input? One of the mouse buttons would seem to be the best solution.
I guess there could be some 'spare I/O' pins on the CPU, but this would mean dismantling the unit.
Other alternative could be to hack the USB keyboard driver to read a key for the input and drive the CAPS or NUM LED for the output and use a keyboard with 'additional hardware interface' for the infrared capability.
Once the hardware is working then its just software.!!

Paul