After studying the situation and being advised against replacing the floorpan myself I put the car up on stands and checked the level to make sure it was within tolerance to remove the existing floorpan. Full disclosure------YouTube video was very enlightening and helpful in starting down this road. Although no one did a Comet, there were several with Mustang and Falcon videos.
I got some 1" X 1/8" angle and welded in crossbraces to the rocker flanges to help steady things.
Using my air saw and an impact chisel I started cutting the offending floorpan out.
Working in small pieces I slowly cut out the entire floorpan so I could prep it for the new one.
The above photo shows how I cut the rear vertical panel to get the new floorpan to seat at the original seam joint.
The car is now ready to prep all the mating surfaces note how the rear torque boxes are integrated into the system.
I have the new floorpan and subframe connectors in hand at this point to help the decision making process.