I don't think your hutch size is inadequate at all. He has access to both hutches? Top and bottom? If so that's 2 4' hutches and then you are going to attach the run on top of that space. I think that's adequate for 1 bunny by himself. Bunnies do like to have company, is there any way you can rescue a spayed female for him to love? He won't notice the lack of attention from you guys as much if he has a friend.

Where abouts are you located?