A new home and you didn't have the HVAC in the estimate? You took the word of an outside salesman? That's why you hired a contractor in the first place. He goes out and gets the price from his subcontractor and then you agree to it, that is shown in his estimate.
What happened is when you bring in your own subcontractor away from the builder. You become the general contractor. It is all on you to rectify the problem with your HVAC guy.
If you had left it to your home builder he would have solved it for you. But now it's leg work that you don't need. Sorry, but take your medicine. Call your HVAC "salesman"and squeak till you get the grease.