The air that comes out of the 2nd floor measures 156 degrees while the downstairs only measures 99.5 degrees.
You have clearly identified the problem. In fact I am inclined to believe that you have at least two problems. First, the furnace is running too hot due to insufficient air flow. I look for oil furnaces to deliver air at 140 degrees and gas furnaces to deliver air at 120 degrees or less. If the gas furnace is a high efficiency condensing
type, the operating temperature is fairly critical and they are designed to run cool compared to furnaces of yesteryear.
Second, it sounds like the insulation on your ground floor ductwork is crushed.
I would not close any second floor vents as your furnace is already running too hot due to insufficient air flow.
I think I'm going to add a return near the baseboard on the first floor. I can pull this off pretty easily since the furnace closet in the garage shares a wall with the living room. I figure that I could shut this new return off in the summer and have it open in the winter to pull the cooler air from near the floor. I'm also thinking about adding another supply register in the living room through the same wall.
These are both good ideas.
If your system has an A/C cooling coil, you probably need to have the blower wired for high-speed year round to over come the air flow resistance this poses in your system.