How do get my key to start my car again?

I should start by saying it is a manual, ford focus mk1
Y reg. Its the 1.8l petrol 3 door version.

So, i took my heater controls off my dash to replace my blower switch as it was faulty ( like in most ford focus's) and when i was done i thought id reprogramme my key ro try and fix a locking issue i have with my key fob. So i put the main key (one with the remote fob) in the ignition and turned back and forward to from position 1 to 2 4 times to enter the programming mode. It beeped once, i then pressesd the locking button. It beeped again. I then removed the key and tested the locking. It didn't work. Oh well i figured.

Later. Upon going back to my car, neither key will start it. The electronics come on, and the immobilizer light turns off after being on for 3 or 4 seconds, then when i turn the key to ignition, all i get is the starter motor ticking, no engine turning at all. I have tried disconnecting the battery for 5 minutes and still the same. I have also tried the key programming again, to no avail.

I would have thought id accidentally unprogrammed the keys, but you should need 2 keys to unprogramme any, and the immobiliser light switches off, with surley indicates that it recognised the key?! So i'm completely stuck. Any ideas?

The Ford immobilizer system is ironclad, especially compared to the GM systems. It somehow got confused and will require an automotive locksmith or the dealer to restore it to sanity.