Hey,
I've got a 2004 Focus SR hatch, and had an unfortunate incident - my keys went through the washing machine. For some reason the remote wouldn't work after that. I bought a new remote module from my dealer and programmed the car to accept it.
The re-programming procedure is quite easy. If your Focus is a manual, check the handbrake is on, and put the car into neutral (so you don't accidentally bunny-hop the car). Insert your key into the ignition, and turn from off to ignition 4 times (you should end up on ignition on the 4th time). You have about ten seconds to activate the new remote. Just press any button on the remote. When finished, turn the key to the off position. Your new remote should now work with your car.
Good luck!
NateD, January 2007