Yes the newer units are a little noisier. Its not noticeable to me due to decades of high decible worksites. But if your wife has sensitive ears then she would probably really notice it. She would love steam or hot water heat.
You are correct that it takes a few years to get your funds back with the highest efficiency furnace available. I presume you are still active military and must still travel a lot. You would not have enough time to recoup your investment through savings only, however, I would reccomend talkng to a realtor about the increased resale value of your home with the higher efficiency furnace. It may also make your home more marketable in the event that real estate cools off before your next move. Just some things to consider.
Good to read that you have found a contractor you feel comfortable with. Hope he keeps your trust. There really are a lot of good honest ones out here.
Work hard, Play hard, Sleep easy.