Assuming the repair is successful, I highly doubt it. If there is a clearly defined fault and the dealer identifies and rectifies this problem then they have fulfilled their contractual obligations.

Then the question is what is the point of the SoGA if it has been sold with a fault? Which is where I am getting confused.

The point is that the dealer is obliged to rectify the fault at his expense. You can only reject a car if it is is 'unfit for purpose'. A fault (even a serious one) doesn't in itself make a car unfit for purpos because if the fault is rectified, then the vehicle is functions as it was advertised.

I don't understand why you would 'lose confidence' in the car if it has a reconditioned gearbox fitted. The recon box will be guaranteed.

You travelled 250 miles to buy a car and never inspected it ,what shims were missing,and you drove 250 miles with the car making noises why did you not take it back when you first heard the noise,You will find if you study the soga regulations and look at tribunal outcomes you do not have much chance of rejecting the car but there is always a chance.

You did not expect the car very well or take any notice when you test drove it you can hardly hide an oil leal or noises or did these not occur until later in which case how would the dealer know .You still have not explained the missing shims if these are the anti squeal shims then with certain pads these are not required. and what has 29years got to do with it my wife has had cars for 33years but still has problems remembering where to put the fuel

.I hope you have a succesful outcome to your problem the dealer seems to be doing his utmost I would wait and see how the car turns out after the work has been done.