Quick update ... I've finished the job, the bike is back together and starting very nicely thank you :)
Here's the new battery in the new box, after a coat of paint (black Hammerite of course). I used a large cable tie as a retaining strap.
The new location for the fuel pump breather pipe. The dirt on my bike is shocking! Bloomin hard to clean back there though.
The new route for the fuel tank balance pipe. I made a cock up and cut the original too short, therefore this is a different bit of fuel pipewith a similar internal bore. No reasonwhy you couldn't use the original though if you measure correctly :)
And the new location for the fuel pump. I think I may revisit this soon, and try it with the pump rotated though 180 degrees, so that the breather comes out at the back. As it is, the breather rubs slightly on the plastic part of the bash plate (you can see a mark on the pipe already).
One disadvantage with this new set up is that to remove the battery I have to remove the box from the bike, there's not clearance to lift it out in situ. However, that's not something you need to do every day so I don't really think it'll be a problem.
My main lingering concern is that a serious impact to the bash plate might damage something because everything is crammed in so tightly behind it. I'll just have to keep an eye on things and check it thoroughly after I go off road.
Does anyone know if a Touratech bashplate gives you more room in the battery area? Or maybe I'll make my own - probably quicker than ordering from TT