It would cost virtually nothing to raise the roof so that the entire first floor has a uniform exterior wall like the one I posted. Then you would have so many more options for windows in the space above the garage. And it saves you having to deal with 6' or 7' walls on any of those rooms. I think half of the arguments you have had about the master suite area have some sort of discussion about either 6'/7' walls. If you raise the roof line, you could also do a shed dormer in the back, and have a beautiful second floor space above the master, which is where I would put an office. So your second story above the main house would be two bedrooms and a bath, and the space above the master could be your office, with nice, big windows that you can shoot out of (which I think is dumb as shit, but Im thinking of you here, not me
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It would look better, too. The elevation you have looks out of whack..almost like there was something just tacked on to the side of the main house.