Well, got the muffler on, a bit of "encouragement" needed to make the plate bracket and muffler bracket meet but it's there now, thanks H2QIK.
On a side note, after all the mucking around I went to start the bike and...tick..tick..tick...nothing! Pulled everything apart again (fairings etc.) checked under the tank where I had removed the exhaust valve cabling, checked all fuses. Still played up, so rechecked everything, the dash even showed up an E3B code which translates to ECU problem no less!
Went to start it again and it was trying, so checked the battery level - 10.4V, flat battery!!
I'm thinking the battery may be old stock from the dealer, this is a 2015 H2 but still they usually put a new battery in at owner pick-up. I've got it on charge now. It has made me recall a couple of times recently when starting it and how sluggish the turnover was for a couple of seconds.
I have a Lithium battery in the shed that I had used on the zx12r, I may give that a go,