I'm with you.
I deal with these same issues myself. I've developed increasingly severe reaction to gluten. Anxiety comes and goes. Z12 helps though i haven't bought it in a while.
You've decided you want to feel better and that's step one.
First, get rid of the sugar and obviously the grains (see below video). SCD is a good plan to follow - Body ecology diet is an even better option as it heavily stresses fermented foods, and discusses the connection between gut and brain. If you can learn to ferment your own cabbage your gut will be in tip top shape in no time - this is basically non-pasteurized (raw) sauerkraut. Plenty of how-to's on youtube. I won't say it's easy, but after a little trial and error you can get it.
Feeling better takes the realization that you can't eat like the average person, and the attitude and determination to make a change.
I've found foam rolling (and even more intensive trigger point therapy) to be invaluable when getting back into the swing of things. I don't know if this is a gluten thing, or what, but I have insanely tight muscles. I think it comes down to dealing with and controlling inflammation from foods. It's the inflammatory nature of the carbs that cause the gut and brain issues you face, and I would venture to say probably tight muscles, lowered testosterone, low vitamin d status (digesting gluten decreases blood Vit D.... this lowers Testosterone as a result), impaired immune function, mood, and recovery, and malabsorbtion issues to boot (all tightly inter-related, no pun intended). All of that depends on the severity of the condition, but you likely suffer to some degree from many of these. It really pisses me off that others can largely eat gluten and get off scott-free, but I digress.
Here are a few training and nutrition tips:
1) I have to do a very thorough warmup on leg day regardless of my overall fitness/conditioning level. I usually prefer to do a warm up consisting of 5 min light cardio followed by 20+ minutes of intense soft tissue work. This alone makes me feel pretty great.
2) Eating right and training gets me the rest of the way to feeling awesome... assuming I can find time to train and cook the foods i need to stay healthy. Speaking of which, minerals. You need minerals and vitamins. I'd bet you have inadequate levels of many and would benefit from elitepro or the like. Supplements are not critical and you can do it with whole foods, if your digestion is better. Supplements only supercharge the process.
3) I don't like total body training as each session doesn't allow for enough volume, or gets too lengthy. Similarly, traditional body part splits can be a bit too intense to recover from, especially for someone with a compromised immune system (sorry, but if your gut is damaged, your recovery will be hindered). My split I like is push, pull, lower. My advice in this paragraph is probably the least important, as I feel any program you like and stick to is what will work best. What worked for you in the past?
4) Coconut oil is my best friend. Calorie and energy-wise, it replaces/displaces a ton of traditional carbs, and is also great for the immune system. Without as much carbs, and by incorporating fermented foods, your gut has a tremendously better chance at healing. I can give you more nutrition advice, but I would honestly say displacing the carbs that cause your condition with healthy fats would be #1.
A lot of great info summed up in this video "Loren Cordain - Origins and Evolution of the Western Diet: Health Implications for the 21st Century" http://www.youtube.com/watch?v=5dw1MuD9EP4#t=3048
PM me or reply here if you have any questions. Best of luck.