The angle grinder won't help on this one. I was measuring all the relavent dimensions and the barrel on the nut is 50mm which wouldn't fit under the stage even if I removed the entire flange. Not sure why it's so much bigger than other people's nuts. I have another 25mm ball screw and the nut on that only has a 40mm barrel.
Misumi actually sells height adjustment risers for linear rails so I guess I'm not the only one with this issue. I might have been tempted to buy some of their machine parts if their website wasn't so frustrating.
I'll definately post some pics when it is finished. I have been resisting the temptation up until now as I wanted to make sure it all works first.