First of All:
HomeDepot allows the contractor to provide man power for the 10 SqFt of space in the building. For this the contractor has the right to sell you an air conditioner and furnace. Now the contractor is responsible to man the store at a minimum of 40 hours per week. The contractor pays this person $10.00 per hour (Called a LEAD Generator) to talk you into allowing their salesman to come to your home for an estimate. Now the salesman depending on the company earns from 8% to 10% for making the sale. The contractor pays the salesman this commission and then pays HomeDepot 10% for this wonderful opportunity to do a lousy overpriced installation for you. Now the contractor has to make a profit on top of all of these other costs. What part of you have been had don't you understand???????????
Second: You have a very difficult installation due to the age and construction of your home. You absolutely need to have a contractor that has some idea of heat loss / heat gain calculations, proper duct sizing and how to install it correctly.
Third: It sounds as though your insulation is well below reasonable standards complicating your comfort problems and operating expenses.
Good Luck, you have been had!!!!!!!!!!!!!!!!!