If you're planning on keeping your new rig for just a few years, you can get by with just the rubber flooring.
If you're going to keep it longer you would want to, at the very least, add a 3/4 pressure treated plywood to the floor. Use a roll of 30# roofing paper to make a pattern so you can cut the plywood to fit perfectly, the first time. Next place the pattern of roofing paper back into it's place in the van, and then install the plywood over top. This will add extreme integrity to the entire van floor, and will provide some insulating qulities to the van floor.
Remove the insulation from the rubber flooring, and put just the rubber flooring back (you don't want to drill up through the rubber insulation when installing your equipment - trust me).
Now install your equipment.