It is very easy to upgrade as much as you did and since you agreed to these items, you are asking the builder to give up profit on a contract and changes that you openly and willingly agreed to. How would you feel if your boss told you 80% of the way through the year that he wanted to reduce your salary?
Renegotiating the price is not a change order. A change order is if you decide you want to add/take off something on the house and has nothing to do with the purchase price. So look at it this way,you won't get a better deal unless you ask. Contact your builder and discuss your concerns. Ask them to give you a better price on the home, and have them give that number. The person who gives a value first is in the worst position. Once they give you a price, then let them know what would make you happy. Come to a happy medium if possible.
We have a changed market here in the Twin Cities and the builders know it. The last thing they want is you to walk when this house is closing in a few months, so they would be stupid to not negotiate. Oh, and one other piece of advice, take your concerns to a higher person in the company...someone who can make this decision. The model agent will tell you "no", but they have no authority to do so. Speak to someone in management, or a President / VP type.
Good Luck, I might be in your position in a few months. Feel free to contact me if you have any additional questions.