Is there anyway I can buy or make an extension for the cord that connects the speakers to the sub?  I'd like to put the sub across the room, but it's way too far away for the normal cord to reach.

http://www.partsexpress.com/webpage.cfm?&DID=7&WebPage_ID=25

Take a look at this online store, they have all kinds of do it yourself parts for electronics, even RCA cords. I made my own DIY power cords from wire and plugs from the local home supply store and they work quite well.

If you can find an S-Video extension cord you should be fine. At least I'm pretty sure they're the same plug style. You might have to pull some pins out with some pliers though. Just keep in mind that extending the DIN cable can possibly add noise to the system.

Another idea you might try - though probably not recommended by Klipsch - is to remove the amplifier from the subwoofer and then simply run speaker wires from the amp to the subwoofer driver. You'll have to close up the hole that the amp was previously filling, but that should be as easy as a small wood panel cut to fit in the same spot. You could then put the amp in its own wooden box near the computer or wherever is convenient.