I hate to tell you this but that trapped feeling could be the source of most of your issues. Stress has a profound effect on both autoimmunity and your resistance to illness. It can directly cause depression too - look up "learned helplessness". And of course your adrenals aren't working well in a chronic stress situation! Remember that too much cortisol is almost more likely than too little, and high cortisol directly causes depression. Unless you had an abnormal 24-hour salivary cortisol test, the herbs you are taking for adrenal fatigue (assuming that such a thing even exists which is questionable) may be pushing you in the wrong direction.
I am finding acupuncture helpful for depression. You could also try some of the milder remedies like 5-HTP or St. John's wort (either/or, not both, and not if you're on a prescription antidepressant). It's tremendously important to get enough B-complex in a high-stress situation becasue you will use up your reserves. If you tolerate citrus, have an orange a day for the natural vitamin C too. Make sure you are getting enough omega-3 fatty acids for proper immune function. A couple fish oil capsules a day can work wonders for your state of mind. Also ask your doctor about vitamin D testing as low D can make you feel worse and lower immune function.
Sometimes doing little things for yourself can make a difference. Buy flowers, have a nice soak in a hot epsom bath, get a massage (particularly helpful as it will release some endorphins), or splurge on something small that makes you happy. My favorite little treat is an expensive bar of super-fragrant soap for my morning shower.
You must exercise, no matter how tired you are. Get out of the house and take a 15 minute walk every day, ideally after dinner so it helps your digestion. If you crank up the pace and walk quickly or jog, you will get more endorphins into your system but I know how hard moving fast is when you are tired. Even a moderate paced walk will help.
While you do this, look at how you can get out of the trap. Remember that whenever God closes a door, he opens a window. It may be that the solution will present itself if you can treat yourself kindly and clear your head for a bit. If you can get clear of the stress you may find all these health problems melt away. (You wouldn't believe how sick some Ph.D. and medical students get - this is how I know about the effects of chronic stress on health.)
Oh.....this is very good, Skylark! I think all your suggestions work better than being over the top concerned about sensitivity and worrying about all the gluten in the world. You need to relax if you want to heal and absolutely exercise. I took my recovery up a few notches when I started weight training and cardio. I can go into a session feeling crappy and tired and feel like a different person when I am finished. It also really helps with digestion, as you said. You have to do the whole package and keep it up and before you know it, you start feeling much better.
As for med students and stress, one of my doctors popped with shingles, at the age of 28, because of those long hours as an intern. She said if the training doesn't kill you, you get to graduate.