I think I may have tracked down at least part of the problem. I carried on disconnecting the drive shafts today and the problem was still there so I bit the bullet, dropped the exhaust and then the prop. With the prop shaft out, the car runs perfectly smooth up past 60 in 5th with no issues which confirms that the flywheel, clutch and gearbox aren't part of the equation. Here's a pic of what I found when I inspected the prop.
The diff end flange on the prop has a raised section which mates with a recess on the diff input flange to ensure it is centralised. As you can see, there is yellow paint stuck tight on the flange now which is the torque paint from the diff input pinion nut. This means the flange must have been tight against the input shaft end and it's therefore likely that the prop wasn't seated properly even though the bolts were done up tight. It may even have been affecting the pre-load on the pinon nut though I suspect it would take a bit more than that.
I'm going to send the prop back to the manufacturer and get a recess cut in the end and also get him to recheck the balance, run out, misalignment and generally reconfirm the measurements from my drawings.
I now have the fun of putting all the other disconnected parts back on the car. Having the car up in the air while I'm waiting will give me chance to improve a few things I'd put off until after the IVA such as the gearbox and exhaust mounts.