Thanks all!
The digging box has an entrance at the bottom of one of the sides and also the big hole on the top, so there is enough space for ventilation - and he does have another place he could make a nest if he wanted, so I guess he's fine and I needn't worry!
I'll look into the dwarf food mixes. I did want to try and keep them both on the same base mix but obviously if Joey can't eat it, he needs something else. I'll see how he gets on with the addition of the stuff from Rat Rations which should be here tomorrow I reckon.
I've made a make shift water bottle stand for now but will look to buy a proper one!
Yes, Rupert loves his new wheel! And guess what, no peeing in it