It is niegh-on to impossible to seal that area at least on an HT...don't ax how I know that.  There are just too many openings and they do not lend themselves to being easily plugged up.  I think the big one that you are talking  about is a very odd shape made up of the rear seat support, the wheel well, and the quarter panel.  Very difficult to seal that.

The best approach for me was to do everything I could to make sure the trunk lid seals properly.  I was getting exh stink in the car and discovered a gap in the deck lid gasket right above the gas cap.  I fixed that and filled a couple of other trunk holes with dum-dum and it took care of the problem.

As for noise, you can make sheet metal pieces that screw down and fill most of the hole but you will never have a perfect seal.  Use any of the popular noise suppression products over the sheet metal to reduce the noise.  I made a steel panel that filled the big hole behind the seat on our HT and covered it with some noise deadener stuff.  It helped a lot.

BB