Well just in case anyone is interested, my mate looked at the car this evening and it looks like it's a problem with the fly wheel! The only engine faults are 4A74 and 4A79 which are the glow plug module. The engine isn't miss firing and all the injectors are fine. So like I said originally, it does feel a bit like a misfire but not if you know what I mean. It looks like it's all been caused by the flywheel failing and so is now unbalanced causing the real rough running.
It's a bit of a concidence as he had another bmw not very long ago with the exact same symptoms. They suspected that maybe it was the timing chain so stripped it all apart to find it was absolutely fine. It was then they noticed the flywheel had siezed. Put a new one in along with a clutch and good as new!