Perhaps this would provide a custom fit
"hole filler" for your transmission tower floor opening. You might be able to use the center cut out section to form a similar surround pad for the parking brake lever.
I think you might be able to use automotive weatherstrip adhesive to glue them to the underside of the floor pan to keep them in place, or you could leave them free floating. The floor pan installed on top should compress them to hold them in place. And if you decide to go ahead with an original style ribbed floor mat (I 2nd 46Sparky's "floor covering" suggestion), the rubber mat would cover the oversized floor pan openings and hide the rubber pad too.
