I just today finished fitting my passenger side floorboard and found it simpler to just put the patch panel over the seat riser. If you cut the back of the floorboard to cover only half the seat riser you can run a bead there. I'll probably run a couple 1/2 beads there and do a continuous bead underneath once get the whole mess tacked together and off the frame.
In case you're interested,
HERE'S the way I'm approaching mine which is in just about as bad a condition as you will find. If I lived out west I would have just junked this rusty box and bought a good cab... things here get pretty rusty.
