To build muscle, you really have to eat a lot of protein. It can be difficult to eat enough! Some folks recommend 1 g per pound of bodyweight (particularly if you want to build muscle), and you shouldn't get less than 1 g per pound of lean mass (your body weight minus body fat), particularly if you're lifting. I'm doing a fitness challenge through my gym right now and we're working through a lot of that. The best thing would be for you to work with a nutritionist and let him/her know what your specific needs (Celiac) and goals (gain muscle mass) are. As a relatively small woman who's used to trying to limit what I eat (calories and otherwise), adding lots of food to my daily meals - particularly meat - has been tough. I've added a lot of deli meat because it's easy (and because I don't have any problem with blood pressure - the salt in deli meat would make it a more difficult go-to for some folks).
I do a variation of CrossFit and we work to failure pretty often. I'm still dealing with what I think is a level of exhaustion that doesn't match my physical effort (so I think something else is causing me to be more tired than I should be), but I am seeing gains in strength - which obviously makes me very happy. SLEEP is super important. It's when your body heals itself, and builds muscle. Let yourself sleep as much as possible - turn off the TV (or computer, or cell phone) and go to bed early. Drink lots of water. I've been diagnosed and gluten-free for about two years, but in the first year I just ran - I couldn't imagine lifting weights I was so tired, and running was something I could do on my schedule and at my pace. I did a half marathon last spring and another last fall and then decided it was time to get stronger.
In terms of healing time before you get back to training - just listen to your body. Personally, I never stopped moving - no matter how tired I was - even though I did scale back on length and intensity. If you need two days off after a tough workout, do some stretching or yoga instead of back to back tough training. If you feel great, go for it (but listen to your body again in recovery - after the workout!). If you don't feel ready for tough workouts yet, ease into them. And don't be hard on yourself mentally - remember that you're healing on the inside, and after a while you'll be able to push yourself harder.
Please be careful of the high iron - I found out recently that I also have something called hemochromatosis. "Normal" bodies shed excess iron. People with hemochromatosis store the iron, eventually in their organs, which causes all sorts of problems. The good news is that if you can catch it early, it can be monitored and very easily treated (essentially by donating blood or just having it drawn).
Hope that's helpful!