To the OP, did you ever get this done? How is the Flirc SE working for you?
I am fighting the suspend/shutdown issue myself without the SE edition, and I am thinking about going to an SE edition (hardware control, solid state switch). If you want to extend your IR sensor signal, you need to use a shielded cable to do so. Twisting the wires together may work as well, but it will depend on the frequency of the possible interference within the computer box.