You can put in new sheet metal floor in the trunk and then drop the fuel cell through the new floor so that it hangs under the car in about the center and have space to run the pipes on either side. Don't use a poly tank for this; use a metal container tank. Add a light stone shield on the front and some heat baffles on the sides and the fuel cell will be good. You might even be able to turn the cell with the long dimension front-to-rear and offset it a bit to one side for better space management.
The tank filler will be in the trunk; there are extensions and fender fillers you can use. Don't use a Monza flip top type; they have a bad habit of popping open in wrecks. I personally would put the filler in a metal tube from the fender to the top for protection. I would also put a metal shield over the fuel line out of the cell and any fuel pump in the area; good racing practice is to always have a complete metal shield between the interior space and any components carrying fuel.
With the cell dropped under the floor, you can still stuff in a spare and your clubs. Here is the general idea: http://www.popularhotrodding.com/features/1311_1968_dodge_dart/photo_10.html
There are also some spare-tire-well-shaped cells around....