$2,500 sounds more than reasonable to me.

Sounds fair. Do it now and you can move in and enjoy your kitchen and not worry about future renovations.

You could also do 42" cabinets with space to the ceiling, and not have the "simply plywood + crown molding". With the low price of $2.5k, and that description, I'd want to see what they are talking about. It could look good. Or it could look like a basic builder's special 1990's soffit, which you would have been better off without. You need to see a pic of what they mean by "simply plywood + crown molding".

I would not do the 36" cabinets with a 9' ceiling under any circumstance. Putting in a stack on top is expensive to begin with, and even more expensive after-the-fact, like, really expensive. And it will be difficult to match the new stack with the existing cabinetry. And if you end up leaving the 36" cabinets as is, you will be forever regretting not going with the 42" cabinets.

Assuming base cabinet height of 36” and backsplash height of 18”: 42” uppers will leave 12” dead space; 36” uppers will leave 18”.

In my opinion, 12” is too tall an opening to be filled with trim in new construction. If these were existing cabinets that you were trying to make the best of in a budget-conscious renovation, then that’s something else.

Is your goal to not have any open space above the cabinets? If so, why? What cabinet brand are you using? Have you priced out any alternatives like 36” + 12” or 39”?

How tall are you? How tall is your wife? Who cooks?

I’m building and the 42’’ option was more than yours. I live alone, am 5’5’’ and will never use the top shelf in my 36’‘ cabinets, so I spent money elsewhere. Even 42s didn’t go all the way up to the 9 foot ceiling and IMO looked only slightly better. Is there a model you could look at first?