Mike,
You could indeed drop the tank flush with the frame rails, I didn't because I don't like the look of the tank being visible from under the back of the truck. The filler neck is a rubber tube with an annodized metal neck that bolts to the tank. You would need to modify this neck to be longer using steel tubing. Then the notch as shown in my pictures would still work. Keep in mind the cross sills are more than 2 inches tall, thus the floor is over 2 inches off the frame. This would still give room for the fuel filler rubber tube.
You could still move the tank up though and modify the cross sills by notching them to clear the tank and tank supports. Then you could use the standard bed boards and brackets but would need to install the floor before the gas tank.
I made a CAD drawing of both mounting versions, flush / recessed, to get a visual of how this works. Check them out at:
http://community.webshots.com/user/lakeroadster/tags/automotive/photos
