After we tore the flooring out, and got to the steel box at the end of the rainbow (so to speak), it was time to lay some new plywood. A Home Depot run supplied us with two sheets of 3/4 inch CDX plywood. We prepped the floor by grinding away broken screws, mopping and bleaching the steel box, and filling holes left from hardware with simple silicone caulk.
The sub-flooring under the bench seat and the counters had to stay, but getting a close cut to the structure was very difficult and producing a straight cut ended up being impossible for us, given the tools and skills at our disposal. Measurements through this area were many, but we ended up needing to cut multiple times anyways.
Chelsea, Shawn, and I tried really hard to get all our cuts right, but in the end it didn't make much of a difference. Right angles and straight edges didn't play nice with the hacked up remnants of sub-flooring.
Getting the pieces to fit tight and right was laborious, and accomplished through trial and error. Eventually, our carpentry resembled sculpting as we traded measuring tapes for sharpies and made blade-width cuts to fit around weird ridges.