Thanks for the input guys, I have had a chat with my mate that did the FEA on the rear end and we have come up with a solution but I just have not had the time to do much during the week.
The tube has now been notched giving full clearance to the diff. You can see in the photo that it is bolted in place in the correct position, temporary spacers made with tube are there until I get the proper ones made.

[/url]
I then spent a little time making a patch to weld into the area that was notched. This is 3mm thick and the tube is 2.6mm wall.
I bent this by hand with nothing more than a vice and a hammer, it took a while to get the curve to match the notch.
As mentioned before I was worried about reducing ground clearance if I added material to the bottom of the notched tube. So I placed the cradle in the car to take a look and I don't think it will be an issue at all as its not the lowest part of the frame.
So the solution will involve adding to the bottom of the tube, there are a few ways I could do it, some easier than others but maybe less aesthetically pleasing to the eye.
This weekend I hope to get it done so I can continue on with the rear diff mounts.