We are doing 17" glass doors on top of 32" solid doors with 4" moulding for our 9' ceilings (custom obviously, but you could get close to that with standard sizes). They are inset cabinets sized to have the top doors be square, and to have our highest reach (we're both 5'5"ish) without a stepstool be the top shelf of the lower cabinet, so that we only need the stool for the upper cabinets.

How soon do you need to decide? I can post our pics when they're installed next month, but that might be too late...

Definitely stick with the larger window. And take what your KD says with a grain of salt. Others might know better about putting stacked uppers. I did like the look as well but I didn't want to pay for the extra boxes as well as wanted a more casual feel to the kitchen (I find the stacked cabinets a little more formal, as well as really nice but that is just me) so did a taller upper with a gap on top that houses some older vases and pottery I love.

Regarding counters and cabinets - as long as the material choices work together in your eyes (compliment each other, level of contrast you like, etc.) and you think it will work for your layout I think you are fine with whatever choice you make. I don't agree with a rule that you have to keep the counters the same if the cabinets are the same - I think it is just her personal preference and you need to develop your preference. Some say if cabinets are the same, then one counter should be different, other say if the cabinets are different you should NOT have different counters. You'll get yourself dizzy with all the conflicting rules...trust your instincts (or that of a really good friend :)

why don't you get the taller uppers?
here are ours...we have 9' ceilings also.

I think taller uppers would look less busy, but the stacked look has its pluses too.
I'd skip the drawer in the corner as it will be too high up to really see what is in it.

Have seen a style of custom cupboard door in which there's a single cabinet to ceiling but glass in door is only positioned in front of upper shelf of cupboard. Very attractive, gives "class" to the room, but is surely cheaper than a separate second cupboard and door. Glass was only about 6-9 inches square, a rather mod or craftsman look.

Missed the other questions---yes, I'd skip the drawer too. Personally I'd never use it since it would be hard to see what was in it.

Saw a great kitchen with mixed counters the other day---all cabinets were fir, but they did an island in soapstone and perimeter counters in marble. Worked beautifully. We are mixing wood and stone on two sides of the kitchen, as much for cost as for anything.

I'll send some photos of our kitchen when it's done....hoping for Thanksgiving! :) but in the meantime, here's a link to one of my inspiration kitchens for stacking the cabinets. I asked about it here a few months back and got some photos of beautiful taller cabinets, too. We decided to stack because: 1) our cabinetmaker was not charging us much more for two versus one tall cabinet; 2) we wanted to be able to close off the top cabinets and put infrequently used things there so they wouldn't get dusty; and 3) we wanted to use glass, but we have a little kitchen and most of what's in the uppers is not pretty to look at. So we're putting glass in the top cabinets, and will store serving bowls and such up there. We are also only doing uppers along one wall, which helps with keeping it from looking too busy, though.

Here is a link that might be useful: Pretty stacked cabinets!

Sorry, I'm late to the party--but if you still have any worries about your window and the way you're stopping the cabinets, this may help. (or not... :-p) It's what we did in our kitchen. (which is still not done...) I did reduce the size of the picture, but it still came out bigger than I wanted it to--on the other hand, this lets you scroll and not see the windows above, thus maybe giving you a better idea. :-) I like the way it looks, I think it opens up your room.

Thanks everyone for your advice. I feel much better and am sticking with the large window! Yea!