Hello, It is never a good idea to screw around with something that works. In theory it could possibly work, but will probably have hot spots. This is the reason current best design has seperate systems for each floor. You could try to close off the chute and see if it works adequately. This needs to be done on a hot day. The location of the cold air return in comparison to the stairs may be important. In theory once again air circulation needs to have the supply at one side and the return at the other side. IMO each room needs adequately return air or the room will not cool and heat properly.

At 400 cfm per ton, 1,200 cfm is needed at a minimum. But for returns, it is always recomended to go larger. I use an old formula which is simple and always works for me. Take the total system required cfm X .36, then add that to the total cfm. Example= 1,200 cfm X .36= 432, 432 + 1,200= 1632 cfm. An 18" round duct, or three 12" round ducts will work. Then the return grill area in the cieling or wall should be- 14 X 14, 12 X 16, ect for the sake of noise the bigger the better. The first number in the grill size is the width, the second is the hiegth- so a 14 X 20 would be 14" wide and 20" tall- the stamps in the grill running the 14" width.

I found this note on page 11 of the installation manual under upflow units: NOTE: Where the maximum airflow is 1800 CFM or more, both sides or the bottom must be used for return air. This is saying the bottom return by itself will be enough. There was note under the upflow unit section, but I assume it also applies to a horizontal installation. You want the filter and grill cover to be at least the size of the opening to the furnace. Making the grille bigger is not going to help if return itself is smaller. I don't know how this is going to work with the filter size you quoted. I would think you would need two 14X24 filters. It would be nice if you get get a 4 inch filter instead of the 1 inch. Otherwise you will be changing the filter every month. The 6x6 stud obstruction should be removed and you want a tightly sealed return duct. The return duct should not have a right angle. It should be a curved elbow to make the 90 degree transition. Sharp angles create more air resistance. How big was the original house and AC, and much area are you adding? Most houses don't have the properly sized duct work to handle a 5 ton AC. Do you have confidence in this HVAC contractor?

It maybe the HRV. Call the builder and ask if the heating system is under warranty. I believe these HRV have a device included to prevent air from entering unless the heating or air conditioning is running.