Well I feel like a right plonker now! Problem was when pulling the derailleur down to attach it to the hub sprocket, I had inadvertently pulled the cable loose so the cable was not sat in the barrel adjuster properly 
all seems well now. Thank you for such a speedy reply
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I have never ever ever done anything like that. Certainly not while being paid to work on bikes. And then sat there confused for way too long. Glad it’s sorted 
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Only realised when I put my wheel back on and it was doing the same thing. It’s then when I thought it was something I had done 
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Hey Matthew,
I wonder if you found a way to fix the problem. I just set up my new Hub and tried to index my gears for hours and it’s still clicking and wont shift properly in the hardest 3 gears. I’m also running an Ultegra R8000 11s, which is why I reply to this thread. I wonder if changing the cassette will do the trick, or if there is something wrong with the Hub. Even in the gears that work, there is a constant “bumping” that results in vibration at higher revolutions. It seems to come from the inside of the Hub. I checked and am using the correct adapters for my axle…
Help would be much appreciated! Thanks