Well, since it appears you've already put a good number of holes in this wood, Id just start over. Plus this time, hopefully, if you measure everything out first this time, the sides will be one piece so it doesnt look like 2 boxes on top of each other.
Edit: I went and looked at the first pics again. If you are careful about deassembling your box, you could probably keep the base of it and just stretch it out forwards without having to start completely over.