It was making a rattling noise when it was in neutral and my foot was off the clutch. I found a video where a guy had the same issue with his XJ, I managed to contact him and he told me what he had figured out. Given the work I had just had done, it seemed likely that I had the same issue. Made it a bit quieter (and stopped my crankshaft moving around) but it also turned out that the wrong clutch was put in. That was my fault since I got the parts for the mechanic. The clutch kit was actually one off ebay that a guy on here recommended. Problem was that it was designed for petrol engines so it wouldn't dampen the diesel vibrations enough for the gearbox.
Yup three sizes so you can adjust how much crankshaft end float you have.