My floor plenum connects to a floor duct that runs full length fore and aft under the floor. The plenum that connected to the long duct was collapsed and severely restricting airflow. Also where it connected it actually extended almost half way into the long duct giving more restriction. I propped the collapsed portion open and drilled holes in the restriction. Some improvement but still cycled on the limit switch due to low air flow and overheating the fire box.
The ultimate solution was to leave the existing ducting in the floor and add two 4" ducts. These are connected to the side knock-outs and routed direct to the living space through the cabinet face. One on each side of the furnace.
I now get tons of heat and the burner runs continuous until the thermostat is satisfied.
Not sure this story helps your situation. In the end I recommend just leaving the existing and add more ducts. The heat moves around just fine even if the main heat is now provided mostly just in the central living area. I would overshoot the minimum duct area specification.