I boss of mine has a sprinter and he built a bed platform inside. Under the platform, he can store the kayak (he did have to create a "niche" in the back door for the very tip of the kayak. The mattress sat on top of the platform at the back. By the side door, the platform tapered off to the driver side, providing a place to put "messy" items that he didn't want on the bed.
Since you don't need the bed, how about just making a platform to fit over the kayak? You can slide the kayak in the back doors. Everything else can be storedabove the platform and within reach from the side or back doors. You might want to add some tie down rings to the top of the platform to hold things steady with bungie cords.