Due to the size of the leaf modules they did restrict my choices for orientation and location in the frame, particularly as i had no flexibility around where to locate the motor (ME1003). In the end i modified the frame, but the cells are still mounted higher than ideal, which affects the weight distribution a little. Building with smaller cells (prism or 18650 cells) allows a much more tailored assembly. However, with the Zero, since you are not constrained by the conventional frame you might be able to work something out. Nonetheless, $1000 for the drop in OEM replacement sounds like it might be cheaper than assembling an alternative pack and reconfiguring.
For the electrics I bought my leaf modules, charger and BMS from hybridautocenter in Las Vegas. They were pretty helpful and still are, offering to modify my components for the upgrade.
I would have guessed from your username that you would be the best person to modify your Zero ......