Pay them the money mate - you agreed a deal and that's it. Yes, they made a cock-up but you're still in the wrong. If I were you I would pay the full amount asap, as you do not own full title to the car and legally, it ain't yours. Perish the thought that some representative of the dealership may just tootle around your gaff one night and and take the car away - easy for them to code another key

Do not let this matter drag on and go through the civil courts, you will lose big time and any judgement against you will have a massive impact on your future credit ratings and ability to get any loans.
We all slag of dealers but they also have a living to make and the missing £1k was probably more than their profit in this deal, especially in the current financial climate.
Do the right thing and pay up

Cass