What did your contract of employment state? ie was there any provision on final termination for there to be a withholding of wages pending stocktake?
I suspect not. Sounds to me that you should be telling him/her about the Employment Rights Act (96) and the fact that this would be looked upon as an unlawful/illegal deduction from wages. You should write to them registering a grievance, they are then obliged to respond.
You have three months post termination to take the matter to an Employment Tribunal - which is your legal route to recovering the full sum.
A well written letter should $hit them up a little and get full payment.
PM me if it gets messy.