I recommend 3ft high for runs, as that's a comfortable size for humans to crawl in and rabbits could do a little jump in there too.
It couldn't go on top of the shed, no. I cannot take up the whole shed as well as regardless of the tortoise pens, the rabbit food, hay and shavings are stored in there.
to clean it out, the buns will poo in there and it will need to be cleaned. Also you will need someway of being able to catch them
they can all stored on a shelf in the shed that the buns can't get to
Really don't think I can store a bin full of food, and huge bags of hay and shavings on the shelves! I will try to have a think as we go along. We only get the bunnies tomorrow and we don't have the hutch as yet. For now, I am using the around 5ft by 5ft of the shed, which I have put a piece of wood in place to section the shed off, and leave around 1ft of room for storage. This is only temporary until we get the hutch. They will then have the hutch plus the temporary room in the shed. They will not be going into the run until they are both fixed.
I managed to get a farm bale of hay on one shelf, and they use the others to jump and play on, the big tub I store food in also doubles as a play toy for them to jump on. My snuggle safes, spare toys, litter trays treats and treat hay all go on another shelf. It is possible.
Why can't they go outside until neutered?