Matt, I am planning to use a D1 for that sort of thing - 1996 5 Door, rather than 3, but I am still trying to get the vehicle prepped.
First thing I did was to build the drawers for the back. These effectively bring the floor up level with the top of the wheelarches, giving a bigger area for boxes to be stacked, whilst still giving access to stuff in drawers.
The seats will be split - the 60 will be left in place (there are 3 of us) and the 40will be folded up (or probably removed), and the floor built up to the same level as the drawers.
Not a huge amount of help I am afraid, and I haven't decided what boxes to use either, so I will be interested to see what else is suggested.
Cheers
Mark