I've been playing around with various designs. No matter which way I wrangle it there's no chance of a shower or separate toilet room, even with a dinette/ bed combo.
The van is an L3H3 transit, so a fair bit of height, but the person who is going to be using the van most of the time is not really up for doing any climbing into bed or using ladders due to neck/back/leg issues.
Here is a quick mock up of the queen size (king size in UK) dinette/ bed (dimensions are pretty accurate and take into account approx 2" of insulation all round...

As you can see, can squeeze in a kitchen unit and a couple of passenger seats but that's about it. Rear seats would be removed most of the time and a table of some sort would be there instead. Would have to sleep on seat cushions too rather than a normal mattress.
This is the design I'm leaning towards - still pretty tight but loads of permanent storage when the bunks aren't being used and massive space under the bed and steps to the side.

The overlapping bunks are stacked in such a way that the bed is full height from the thighs up and about 40cm high below that. Taken from
http://www.thismovinghouse.co.uk, who in turn was inspired by similar designs in boats. His van has an extra few feet on mine though.