So this weekend I raised the bed by using the old spacers
That gained a little space
But pulling the bed sides together by making the tailgate catch smaller is also helping as it brings the bed side in rotating the wing up and out. I may need to modify both and then still roll in the inner lip of the wing a bit.
Also I may gain 1/2" or so when I fit the bed, though as my son pointed out the weight of the wood may lower the bed again.
Also not sure why the bed isn't sitting square with the cab, or is it the cab that's not sitting square with the bed? May need to live with this!