My advice would be to make the hutch 6ft x 2ft with two levels, so about 4ft high plus the legs. This makes it an easy size to make as you can get your wood cut into the right size pieces easily, eg lots of 6ft x 2ft and 4ft x 2ft pieces can make that hutch. Use some square and thick timber to build a frame, something like 45mm x 45mm timber. Keep it simple. Then just use rectangular pieces of plywood, something like 6mm thick to build the floors and sides on to the frame.
I would design it so that the doors of the hutch open onto one side and there is a door that opens onto their run on the other side. This makes it easy to clean out as you don't have to move the run, the run can be permanently fixed onto the hutch very securely using long screws. Make the ramp inside the hutch long and a gentle slope. I would keep the downstairs dark with doors that have no openings on them so that they have somewhere dark and safe to hide. I would then have some windows on the top level and leave the top level open with their food area up there.
For the run I would recommend building it using aviary style panels. They are pretty easy to make yourself and quite easy to build together into a run by just screwing them together. Use some timber that is quite thick to stop any foxes etc chewing it, something like 1 inch by 2 inch. Make each panel in factors of 3ft, so 3ft x 6ft or 3ft x 9ft so that it is easy to fit the mesh to as the mesh comes on 3ft wide rolls. Just a basic rectangle will do but with a support beam every 3ft. For the mesh you want to get a LOT and the cheapest place is usually eBay. You want galvanised wire mesh with holes of about half an inch by one inch. I recommend putting mesh panels on the bottom of the run to to keep it totally secure. You can put paving slabs or turf or mats on top of the mesh to make it more comfortable. If you want to make the run easy to get into you can make one or two of the panels hinged with bolts to hold them in place.
