I did something very similar to my first wagon, twenty years ago, a 84 GL.Thy did not have the rear spare.I removed the seat back and bottom and made a plywood hatch/box taking the place of the seat when it was down.Worked awsome.I took the padding off the seat back of my current first gen and removed the seat bottom.I can get everything to spend a couple nights on the river under the seats.I sleep in the back.
I made a custom tarp that tunneled off the back for my GL.It fastened to a roof rack and worked great camping.I wish I had pics.Loving what your doing.