Keeping the top of the platform relatively low like you've done is important to make it comfortable when used as a sleeper. It does limit the capacity of the storage underneath, but it's a good trade-off.
Yeah I ended up lowering it after my initial design once I started test fitting pieces and more importantly put the piece on the top of the second row seats. As of right now the side pieces of the box are 8" with a sheet on top and bottom for a total 9.25-9.5" high. And this give me 7" of height inside the box but I don't plan on putting a tool box inside the drawer. Plan on splitting up my tools into little containers and pouches.
I realize you want to keep it low so that you are not right in the roof of your car, but in your pictures it looks like wear you go from your back seats to the rear cargo area it isn't level? It might just be the pictures???