Window heads are typically higher than doors to capture more natural sunlight. That being said what are the upstairs rooms being used for? If bedrooms I do not think you can raise them any higher for egress requirements.

A bathroom and a bedroom. Based on egress requirements in NH they can be raised, 44" above floor maximum, right now I'm only at 28"

I don't know if I've ever noticed an equal amount of space above and below a dormer window, at least it doesn't stand out that it's a feature. That would require some in-depth detailing or just plain luck. Keeping the heights all at 80" is fine. I think you will not notice as much once the siding, trim, downspouts, shingles, and landscaping are up.

It's more about the proportionality overall of the dormer with the massing and fenestration in proportion to the dormer. I think here it is more noticeable because of all the field space around the windows. And the 17" above the windows appears taller than the 1st floor probably as a result of the overhang not being at the same slope (more shallow on the dormer) and less of a birdsmouth cut on the rafters, leading to the fascia appearing higher.

I do not think the cost and work to raise those windows will be paid back at all New headers new framing really how bad do you think this is . I actually see no big issue

I think it looks great as is. Vertical spacing is not important in the way you are thinking about it -- going up just means losing more light to overhangs, among other things, and the flashing and gutters add visual weight to the space above. Let the project proceed and you will probably never think of this again.

^ agree, I think it is pleasing to the eye as is

It looks fine to me. The overall impression is good. Don't nitpick over tiny details. No house is perfect, I'm sure you'll find some other tiny imperfection, too.

I wouldn't remove the Dormer windows it brings light in that room needs light just like the downstairs I think it looks fine