First,I would weatherize your home all you can; that is where you get the most savings.

I would have someone perform a blower door test for amount of air infiltration. Half the heatgain/heatloss can be due to a high air infiltration rate! Reduce it to a minimum.

The duct system must be optimized; check the linked page for all the information you ought to know before the install. - udarrell

Here is a link that might be useful: Correct Sizing of Residential A/C & Duct System

Thanks udarrell. I have an email in to both folks regarding the Manual S/Manual D, infiltration, etc...

I know I want to replace my windows soon, but my furnace/ac are currently 22 years old and giving up the ghost (freon leak, parts failing on the furnace) so I have to go this route right now, and windows at a later date.

Given that I have to get this replaced now, can you please review the info in my OP and give me some suggestions or advice?

- AngrySalad

I'm also considering gettins storm windows for my home instead or replacement windows, as storm windows will be cheaper, quicker, and there's nothing physically wrong with my current windows (ie. not broken).

Why do we always want to do things backwards? If your heatloss is correct (sounds high to me) and you size the equipment for that load and then tighten up the home the equipment is over sized. Now you paid more for the equipment and the efficiency just went down and the maintenance costs just went up. The most efficient operation is a properly sized unit. Too coll the house efficiently you need to remove the humidity. If the a/c is over sized it will not run long enough to remove the proper amount of humidity and the comfort level is compromised. Cool and clammy.
As stated above tighten up the home first then replace the units. Your largest savings and cheapest long term cost is in the envelope.

Thanks tk03. I understand what you and udarrell are saying. I have a call into a window joint to see if I can get storm windows on my house soon. At the same time, I do need to act on a new system soon, too.

So, let's say I get the house fairly sealed up with storms, maybe new weather stripping around the doors if needed. Then, from my OP, which system set up would be optimal for 2700-2800 sq. ft. home with 17 registers (+ 5 more in basement) and which of the dealers has done an adequate job of sizing my needs?

Here's what my Trane rep had to say about my questions:

"The static air pressure test is not required. Balancing of the dampers can make a nice improvement, without the static air pressure test. The exposed ductwork in the basement can be sealed with foil tape or duct sealer (caulk type or 1 gallon can). Home Depot has those items so you can do on your own if you like. The cost for us to do the duct sealing would range from $250.00 to $500.00 depending how much time it would take. The air infiltration for your home is most likely average, the equipment that I recommended will do the job well.

The duct sizes within the walls cannot be modified to increase airflow very easily. The existing ducts that are in your house are typical for the homes in the area. The variable speed furnace will react to the duct work and adjust airflow. How? Electronically it monitors the RPM of the motor and checks the amp rating and speed settings. If it is not moving fast enough the power level is increased to the motor and the speed is increased. The current furnace cannot respond to the ductwork like the XV95. The TRANE XV95 can move up to 40% more air."

My response:

"I'm just concerned that if I were to make home improvements after purchase (buy replacement windows) that the furnace and/or AC would be oversized for my needs due to higher efficiency, less heat gain/loss from the replacement windows.

At the sizes you recommended, would I be in danger of the AC satisfying the thermostat too quickly or not removing the proper amount of humidity if I were to tighten up the house with new windows, thus still leaving me with warm/cool spots in my house?"

Again, thanks for your help! - Angrysalad

I think the sizing of the furnace is a minor issue and not to worry about it. The reason is the Trane furnace he is talking about is 2 stage heat. So if he installs a 2 stage thermostat then the majority of the winter the unit will run on low heat. This will provide longer run cycles and provide more even heat. I would confirm the input and output of the existing furnace. The new furnace should have the same output.
I didn't see that you mentioned how your comfort was in the summertime. Did the air conditioning run for long periods of time on the hottest days? or did it short cycle?
Going from a 4 ton to a 3 ton is a pretty big drop so I would make sure you are comfortable with that.

Thanks Funnycide.

To be honest, I can't really complain about the cooling in the summer. If anything, I would say it short cycled from time to time, and 2 of the upstairs rooms don't seem to cool off as well as the others (both sets of vents are at the end of the runs) but I don't really recall an issue. I felt that the original AC may have been a little too big and was satisfying the thermostat before cooling all of the rooms. It's more the heating in the winter I have issue with. The overall warmth in the house is just not what I think it should be.

So, anyone have response to the techniques either of these reps used to figure out what system I should have? The measuring vs. the "experience" with using a template, etc...

If you were overall happy with your 4 ton air conditioner then I wouldn't drop lower than a 3.5 ton. It's possible that a 3 ton unit would cool your house fine but I'm not sure there would be a reason to risk it.