as the LED is flashing fast there is a concern with the immobiliser system on the car. If you have a spare key then try using this if it works then you know the key is faulty.
If the immobiliser still won't disarm then check the following fuses, 30, 9 and 36 in the fuse box near the battery. Fuse 30 is a 3 amp fuse and can blow very easily if the car is jump started. Check fuses 46, 67 and 68 in the fuse box behind the glove box as these are for the immobiliser system. When checking all the fuses make sure that there is 12 volts across the fuses when the ignition is turned on.
If all the fuses are OK and there is 12 volts then unfortunately a diagnostic scan will be required to help pinpoint the part of the immobiliser system causing the concern. Sometimes when the battery has gone completely flat it may be a case of initializing the system again but this still requires a diagnostic scan tool to do so.
The immobiliser system uses the engine management and instrument cluster to operate so a fault in either of these systems can cause immobiliser concerns, the most common failure if not a fuse tends to be the cluster but as I said earlier you will need a diagnostic scan to confirm this.
On a separate note your 1.8 diesel Focus has an outstanding recall for a cooling fan issue, your local Ford dealer will carry this out free of charge, the reference number for this is 8C203, if you give the dealer your chassis number they can confirm this for you.
Let me know if I can assist any more or if you have further questions regarding this and I'll reply as soon as I can.