On my WJ I plan to do something similar to this and already have the seat bottoms out with a temporary platform made. But if you already have the seat bottoms out why not pull out the backs also, allowing you to build in more storage? My thought is if the bottoms are out and you don't pack them with you on trips then the backs are no good to have either since you can't flip them up for someone to sit there. Also the backs are around 4"-6" deep, that's just wasted space if they just stay down all the time.
My seat is a 60/40 split like yours so my plan is to build 2 boxes, one for each side of the split bench allowing me to put one or the other sides back in if I ever need to. The box would be kind of an "L" shape with part being in the foot well for the rear seats and then up and over where the seat backs lay when folded down. I would probably put in a divider or trays so each box has multiple compartments. Not sure if something like this would work in your rig but just an idea I've been kicking around that I thought I would share.