I don't know the story behind this, but the wording you used before they started work is important. If you diagnosed specific faults yourself and told them what to do to fix it then if they have done what you instructed them to do the law is on their side. However, if you booked it in and described the symptoms leaving them to diagnose and rectify any fault(s) it can be a very different story.
Example.
Tell them you need a new clutch and upon collection the fault is still there because it was a gearbox problem puts the blame on you.
Tell them your having problems when changing gear and for them to be paid the fault needs to be correctly diagnosed by them then rectified.
It sounds like they have done some work but your car is still not right. In this case the precedent is for you to reach a financial compromise. They've put time and effort (and presumeably parts) into the car and for that they should be reimbursed, however the sum should be less than the sum agreed upon for them to put the car back to running order.
