I've been taking Armour thyroid for about 12 years now, and it was only in the last 2 years that I even knew that you were supposed to take it on an empty stomach! I have stayed on the same dose for several years, except when I was pregnant with my second child and had to increase my dose slightly during the pregnancy. I take it first thing in the morning, and generally have my coffee (2 cups, half-decaf, with milk) within 30 minutes of taking it, then breakfast another 15-30 minutes later, and haven't had any issues from it.

I tried Synthroid but it made me quite sick to my stomach, no matter when I took it. Armour is an animal (pig) product, which is why I tried synthroid (I avoid animal products when I can). Not sure if it would be appropriate for your needs, but you might ask your doc if Armour would work better for you and your schedule.