Going back a little, I positioned the mounts on the frame using the following technique.
I was able to copy the style of the frame mounts on the rear of the Bonneville and I also used the anti-vibration mounts from the Bonneville.
Using the tank, seat and rear mudguard from my Bonneville style kit, and with the over length swing arm fitted I could get two crucial dimensions- that is the position of the mudguard so that its curve aligned with the curve of the rear tyre.
Finally, I lowered the frame down to the point to represent the suspension was about as compressed as possible. This positioned the mudguard at the correct height.
So now it is a matter of figuring out the mounts for the seat, tank and mudguard.
This now left a gap to fit in the battery box. I decided to make life more difficult for myself by insisting that the standard air-box would fit in (should I decide to fit one later), this meant that I needed to squeeze in the battery and ECU et al into the tight space left.
I decided to put the battery (the Z1100 model) between the frame tubes from above, not from the side like the Z1100. This allowed me to use the sides of the battery box to fit the fuel pump and electrics, but it did put the battery a long way forward- and then I could put the ECU behind it- making the ECU box double up as the inner rear mudguard.
This all sounds complicated, but it was a lot easier when you consider that I was using lots and lots of cardboard models. I made dozens. Simple to start with and more and more complicated as time went on.
I used a technique of printing out my computer drawings for each part and sticking them on cardboard- then cutting them out. Over time I was able to add more and more detail- and actually the cardboard boxes were surprisingly strong- certainly good enough to support the actual battery.
I decided to build the real box from alloy and to solder the plates together, however in the end this was a pain as the heat necessary was high enough that as one joint reached melting point, previous joints would fall apart. In the end I used structural adhesive for aluminium.
The challenge is not to commit too soon- every time you consider a new bit of the puzzle the design can shift- for example the bend radius and connector on the ECU loom- the battery box needed enough clearance and the hole needed to be large enough to allow the connector through.
I was pleased with the final box- it looks neat and squeezes everything in- all rubber mounted and solid.

z650/1400 bonneville hybrid.