A second floor hot air return will definitely help. Also make sure that you have good attic ventilation as well. A hot attic will reduce the cooling effect of AC in the second story. Effective options include electric attic fans, a ridge vent, or other methods. Depending on your climate (where you live) heating or cooling may be the dominant factor to consider in designing your system. With AC, I prefer a unit that is a little larger than average. I want the house to stay cool with 20 people over and the oven going for holiday parties.
Another thing that helps keep the second floor comfortable is putting a second layer of insulation in the attic.
I thought that your estimate might have included ductwork.
Janitrol furnaces are the cheepest to buy. That is why many new home construction companies use them. It keeps the total cost of building a new house down. Some may work fine, however many vibrate, make noises, and fall apart after 5 or so years.
I personally like the Trane products, partly because of the quality & reliability, and partly because of my local dealer who I would recommend to anyone.
A final point that most people overlook. If possible, try to locate the AC condenser on the north face of the house. It will run more efficiently that way.