Looking at this I'm asking myself "What must be done to make this work?" The Ag model has a structural panel with a trap door. In order to remove the hopper, the panel comes off the fuselage top and the attachment where the seat back usually goes is disconnected. This is replaced with the removable seat back cross bar. Then I look at the fuselage drawing and notice a V shaped collection of tubing which is welded to the rest of the primary structure in the two place version over the space where the hopper goes. "Why is this there?" It appears it is to tie the wing center section to the aft portion of the fuselage. Aha! 2+2=4! That V tubing structure is doing the same job as the plate which covers the hopper. Conclusion, to remove the hopper plate some form of tubing or other structural member has to go in to replace it. The only question Which I can't answer is "Does the hopper cover plate utilize enough fasteners to be included as part of the structural support for it's frame?" If "yes" then what ever is done with the cover plate must also be done with the frame. If "no" then the frame could be left on and the cover could be replaced with Lexan as a minor alteration.
So Alex, In those pictures is that the hopper frame surrounding the Lexan? Or is that just something holding the Lexan in place?
Fuselage drawing:
http://www.supercubproject.com/drawings/pdfs/A3250005.pdf View attachment 52591
View attachment 52592
My suspicions are that the cover plate is part of the frame structure which is maintaining the proper strength and load path between the wing center section and the aft fuselage. And that the V shaped tubing structure or a suitable alternative is required. Perhaps a bolt in V?