I would price out your cabinets and countertops based on the layout/features you want. They will be the most expensive. Then there is the cost of labor to install which you should be able to price out along with the cabinets/counters and also the cost of removing the old kitchen. Sinks/faucets would you keep those or get new ones?

If this is the route you want to go then I would make sure that they install the floors to go under the cabinets so that there is no size mismatches or issues with covering something in the floor. In Texas this is rare to do so it may be an upcharge and the builder may not be willing to do so, but it would make things simpler when replacing cabinets and some things that may not align.

We may do another sink, however we've found some online that are cheaper than the builder's prices but are the exact same model as their upgraded one.

For the flooring, part of the issue is also that the builder only offers a couple of the ligher-colored wood choices, and that too at a very high premium, so we're considering upgrading flooring on our own elsewhere. However, thanks for the tip regarding flooring under the cabinets, would have never thought about that! What exactly do you mean by "things that may not align"? Is that referring to things like appliances not fitting?

Here is a thought....since the layout and electrical isn't changing in your vision, could you use the builder basic boxes and get custom doors made for the cupboards? Would that work at all? I hear you about spotty granite (ugh). If you are planning to remove whatever they put in, is there a formica or laminate option? I think I'd choose the least option from a price point of view and then if you can use it again elsewhere in the house, formica is relatively easy to take out and cut to size etc - and more DIY than if it is a stone of some sort.

But I think you'd want your flooring to run under the cabinets, so if they install and you want to change the flooring out, you'll be tearing all of it out.

Do you have specific cabinets in mind? Have you talked to that company for a price quote? I think I'd start there and that will give you a good idea of price difference between what the builder wants and the other quote. Counters - well that can be quite a price range so you'd better get a quote on that too. I guess you really need to do some comparison shopping for what you want to get good ideas for pricing.

It might be worth booking an appointment with a kitchen designer who can help you sort through the options available from the builder and other options available. You don't want to spend money twice if you can avoid it so I think some professional help (not some paid salesperson from the builder) might be a good idea to give you some feedback and options.

Look at some posts on Houzz from "The Cooks kitchen". She has some really good kitchen ideas and is willing to share her knowledge generously.

The layout you've shown above from the builder doesn't look bad at all, but maybe a professional can find a way to make the most of the choices available to you and limit some expenses and waste if possible.

Builders make their money on upgrades, so your approach makes a lot of sense.

My suggestion would be to live with the builder kitchen for awhile, so you get a chance to evaluate the layout and how it works for you. You may decide you want something different after living with it for awhile.

You also have probably had to make a lot of decisions. Give yourself time to move in and relax. A good kitchen takes a lot of time to plan.

I think your stone budget for a waterfall and quartz counter and backsplash is going to eat up a good chunk of $40k really quickly. Like others are suggesting, I hope you have time to get some quotes for what you want. If you don’t do this now, it will be a greater headache to do it all later, and at that point you’ll be going without a kitchen while the work is done.

You can save $$ by not doing a waterfall.

That first photo without the waterfall is still gorgeous.

Better to put your $$ into something that really performs a function for you.

You might also think about Corian rather than quartz or granite.

Corian is easier to maintain and repair.

Invite Joseph Corlett into the thread, he is a pro.