A lot of people are talking about the size of the AC. If I understand the OP, it's not the size that's in dispute, but rather the efficiency (SEER).

I hope this house is 800 square feet

OP may not be in a position to walk. When we moved into our new house a year ago the timing of the closing of our sold home and the new house was within days, no turning back.

Unless the kitchen is small $3-4K for granite in the kitchen and 2 baths sounds pretty low. Don't cheat yourself.

I am in the process of saving for new countertops, I got three quotes last year for my small kitchen (all ranging in the $4-6K range with no island). I think taking cash is a big big mistake. Get the correct AC and counters installed now and enjoy them for the next 10-15 years easy. Take cash now and in 2 years when you hate your counters you will pay double to have it installed after-the-fact.

Don't take ANY money. Make them install the better AC system and granite counter tops.

If you do take money, YOU hold all the bargaining power here. You signed a contract that they failed to complete. $5000 is way too low. Start at $30,000 (seriously). You want $30,000, or you'll take the proper AC and granite counter tops. You can always negotiate down, but you cant negotiate up. Dont take anything less than $15000 in cash concessions.

The builder buys in bulk. He has that AC system, and your counter tops, sitting in his warehouse somewhere. He gets way better pricing on this stuff, then you would, if you have to put in granite counter tops after the fact.

Name and shame the builder.

Well....let the builder have a chance to make it right first.

It sounds like the OP bought a spec house but he still has some say in things. When I build mine I was there from the beginning, and specified oak hand rails instead of the standard half-wall. First walk-through came and I noticed that they framed out the stairwell for the half-wall. Pointed that out to the supervisor doing the walk-through and the next time I visited, the rough-in was gone and I got my oak hand rails.

Don't get me wrong, I'm all for naming/shaming if the builder doesn't respond appropriately, but you have to give them a chance first.

2 things on the AC.....That 2 ton unit is going to run .....A LOT with the heat and humidity you get down there in San Antonio and the south wind is blowing. Put it this way, houses around here that are between 1800 and 2200 sq. ft are getting 4 ton units. Unless you spec out a larger size, a builder is going to use the cheapest they can find to meet house spec's. Also, Lennox isn't as good as they once were in the 90's and before. Parts availability has been an issue for them for the past 10 years. Also, from my experience working with AC folks, the higher SEER means higher cost and less longevity. I think with at least a 16 SEER, there are also rebates, but I wouldn't go any higher than a 16 SEER if your looking at getting a cost estimate from another AC vendor for comparison.

^^^THIS!^^^

I paid under $2k for my galley + island granite installed by going to the right wholesale guy/installer.

I'm puzzled as well. When OP signed off against the said options, were they an upgrade? I would think they were. If so, the builder charged extra for them, how much did the builder charge for them?

If it were me and I already paid for these option, I would want them installed. If not, The cost of these items later on becomes greater because you cannot use your kitchen when the countertops are being done, same with AC, so there is an inconvenience factor.

Unless this is a small kitchen, 5k is low for granite countertops installed after the fact.

Minimum I'd be looking for is 10k for the issues described. They signed the contract too to deliver you what you agreed upon. Let the builder figure out how to deliver what they agreed upon. Either as it was specified or at a lower price (and more than 5k - the builder would agree to that in a heartbeat...)

BINGO...

They made an agreement with you and failed to come through on these items....

Make them do it right or walk.

I would hold their feet to the fire and get these discrepancies taken care of before signing off. Also, you have to wonder what else is lacking or missing. Do a thorough walkthrough.

Texas is hot, but it isn’t THAT hot. It’s humid.

You don’t size an A/C unit just on square footage. If it’s well insulated it might be fine.

Yeah that was my thought too....probably cutting lots of corners. I'd get my own home inspector to check it thoroughly! Make the builder pay for that too.

Just because it is a new build doesn't mean there aren't issues right from the start!