Will there be an upstairs? Depending on your budget, I would go 10 in the bedrooms and 12 in the dining, kitchen, gr & foyer. The 12s in the kitchen will give you lots of room for decor on top of cabinet uppers. The changing plate heights will give the home some architectural interest in the front elevation. If you go below 10' ceilings I wouldn't put in 8' doors, They would look pinched. If you go 12 I wouldn't put in 6-8 doors either. My advice..10 & 12 ceilings with 8-0 doors.

The house will have a main level and a basement. There will not be a second story. The main floor is approximately 3000 square feet. What is an approximate cost difference between 6-8 doors and 9 ft ceilings in the two bedrooms versus 8 ft doors and 10 ft ceilings?

Correction. The main floor is approx 3300 sq ft.

$35.00 per door and I'd have to calculate the lumber but i would guess $800.