Yes, install a separate zoning control for the basement. Now is the time. Yes, I think both furnaces are oversized. Makes me wonder if he sized the furnaces not for the heating BTU capacity but for the 4 ton rated blower that would be needed for the 3 1/2 ton condenser. Yes, based on heat gain calc, a three ton condenser seems to be right size, not 3 1/2 ton as quoted. This should be questioned. Keep in mind, 36 KBTUs=3 tons. I would want to know the design temperatures used both inside temp and outside temp both for winter heating and summer cooling. You want excellent ductwork insulation for attic. That's a long way to blow air. You might consider an 80% furnace for second floor installed in attic. This would eliminate the long distance or perhaps insulate attic where it can take a high efficient condensing furnace without fear of freeze ups. The 80% would be a less expensive option. Discuss the options with dealer/GC. Nothing is easy is it? IMO

Cats always seem to need/want to be in the middle of things. Oh, you're reading the paper - well let me lie down on it. On the computer - let me tip-toe across the keyboard and erase your post, making dinner meoooow - well feed me first. Unpacking something - oh a big box which must be for me and string too oh goodie. A construction zone - not surprising. How can you tell I have two of the little critters and yours is gorgeous.

I had a similar situation identical to your planed build 2 months ago for an existing 1995 home. My first recommendation was a separate system. The second was a dual zone system, and reluctantly gave a third recommendation of just ducting the basement off the existing furnace. I agree with David Cary about a separate system for the basement for many of his reasons including my own I told the other guy about , like giving the basement it's own independent return system to reduce sound transmission to the upper levels and odors down stairs. not to mention the simplicity, convenience, and redundancy of a back up if one heater breaks down in the dead of winter at midnight. The unit for the upper floors can be smaller saving a few bucks on the furnace, which can be put into the cost of the second separate system for the basement. The similar house I mentioned was 2400 on two stories and a 1000 sq. ft basement where the owner also worked from home. I did a quick load calculation and determined his new (2017) furnace of 60K Btu's wouldn't carry the basement load and pushed the separate system or replace the existing with a 80 to 90K furnace, he didn't believe me and had a few other people out. They all said the 60K was to small, so he had it replaced with a 80K and duct work for the basement without zone control for $5600. He's still going to freeze his feet off down there this winter..... and won't even be able to kick himself for not taking my offer to put in a separate furnace with duct work for $3800.

Such great advice given to you!!! We are also very familiar with Charleston and Mount Pleasant. Have a daughter and son-in-law living in Park West, Mt. Pleasant. And we have been vacationing in Wild Dunes for many years. My parents have owned property there, as well. I feel like you are getting a decent deal with your house especially with the construction material rises, the square footage of your new home, and the fact that your lot is surrounded and protecting by woods and wetlands. Just a couple of observations to point out. All areas of the country, all subs, builders, etc. are not equal. Upgrades sometimes carry a premium when they are actually overpriced where the builder gets a cut. Talk to your subs before work begins and get everything in writing from your builder!!! We text and email a lot with our builder. These have become useful for us both when work was not done to specification. Threw in the garage door openers (n=2) which is normally a $1,000 option That's sounds bit high. Our Hormann are suppose to be among the very best garage door openers. Very quiet and run smoothly. Two at $241.46 each - Total $482.92. These included exterior garage door keypads. Tile work is expensive! It seems every bit of tile work we wanted done other than a standard 6x6 had an additional cost related to it. Once I understood that I was able to make better decisions on which layouts were important to me and which I could live without I guess this can go with any building process, depending on the area, but our tile work was bid on, and under contract, before any tile selections were even made! No extra cost for different sizes or patterns. - Be ready to spend $$$ on electrical upgrades. It's not glamorous but necessary. We walked the house with our electrician for about 6 hours. We added about an extra 9k to our build, 2k was an additional electrical panel needed for our induction stovetop, the rest was extra outlets, switched plugs, recessed lighting, speaker wiring, etc. Take time in this area So true!!! There will be all kinds of upgrade surprises. And most allowances are never enough!!!