Gearbox knocking or something else?

Hi, bought a streeka hardtop not long ago,,  04 reg, less than 55.000 miles. Previous owner hit a pothole which resulted in her having to change the alloy wheel for another 1 as it was bent. This was changed and also the driveshaft was changed on the  near side. Having this fixed i thought would get rid of the knocking sound, but alas it seems the knocking sound  is now coming from somewhere else, a garage mechanic said it is most likely coming from the gearbox as it speeds up and slows down when accelerating and deaccelerating, im wondering if  the previous owner hitting the pothole has maybe bent the discs or damaged something else? Ive had the offside driveshaft checked and apparently its ok, gearbox oil has been checked and the level  is ok. Its had new oil and oil filter change, and lots of work to the steering wishbones etc before i bought it. Any thoughts?