The piece of angle you're referring to is the rear hold-down plate and the plywood floor fits between it and the rear floor channel
. (In the picture, I incorrectly refer to it as "C" channel.)
The 5" piece of aluminum is the flashing that lies below it. I think if it's in the way, you can pull it out (couple of rivets) and re-install it once the floor is in.
The separation will be remedied once the new floor section is in place and all bolts are installed and tightened. Andy R of Inland recommends additional hold down points outboard of the main frame rails as well to add increased rear holding strength. (Attach 2" angle off main frame rail and run bolt through angle, floor, and curved floor channel).
From the factory, your only hold down points
are on either main frame rail wiith the 5/16" or 3/8" bold passing through the a steel hold down, floor channel, plywood floor, and main frame rail (in that order).
When tying it all back together with new floor, be sure both main hold down points are lined up. (The shell can shift from side to side, even up to 2" or so)
See my pics if it helps any.