Well they're on. A cup of tea helped followed by some more bending and twisting of the lower bracket. Not perfect and the bracket is a bit of a mess to look at, but at least I've a bike on the road. And louder than I expected.
I vaguely recall having the same issue when I first took my exhausts off my brand new 500, I turned out I had re-installed them incorrectly, one bracket goes behind the footrest hanger and one in front of it, I put them together and this caused the back end to miss align so much it was a real struggle to get the balance pipe on, once I figured out what I'd done the were fine again. Check the position of the brackets is my advise.
Done it, and the set I fitted lined up perfect with both brackets on the front of the hanger. The PO had tweaked them that much, the pipes would not line up with the brackets on the right way.