I see lots of spare cubes if I was you Id rebuild it..You have the right idea just a bit small..
I would take the top layer off and make the bottom bigger and I see enough sides to still have a top shelf at one end..
I just built a piggie cage and only used 10 pieces and my cage is single layer and it measures 6 feet square..
Im sure theres enough there to make it nice and roomy for the bunny..
hugs
Kim xx
Please make it bigger. That's kind of cruel. Rebuild it with the spare cubes. If space is an issue, you can even build up, not down (WIth safety precautions of course)