Two ducts Blowing hot air, 4 ducts blowing cold air
Could you add some pictures of the furnace and connected duct work. Are The duct sizes you list round ducts? How long are the ducts from the furnace to the register connections?  Are the ducts insulated? Where are you located since a 4 ton A/C unit is quite large for  a 3 bedroom 1 bathroom house. I would have guessed a 2 to 2 1/2 ton unit would be large enough.