Several phrases stood out as I read your history. They are enough similar to my own issues that I want to share what I am doing, for you to take or leave as you see fit.
I take 15mg of hydrocortisone and 60mg of armour thyroid, my energy is low, i don't recover from exercise well or heal tissues well
Slow recovery and healing is classic for hypothyroidism. From all we've been learning from Dr. Mark Starr and Dr. Broda Barnes, consider that 60 mg of Armour might not be enough. In the old parlance, that's only 1 grain of thyroid. The common range of replacement is 1-5 grains, with most at around 3 grains. Good reading at www.StopTheThyroidMadness.com
very hard to keep water in me
Have you worked with adding regular amounts of good salt to your regimen? The water will stay, plus you will give your adrenals another partner to the hydrocortisone. The right amount for you is the tricky part.
Taking calcium makes me rigid, taking more than 100mg of mag a day give me D
If you find your calcium/magnesium balance, magnesium won't give you diarrhea. I won't say I've "fixed" this problem, but I've had adventures with it. When I started working to raise my vitamin D to the 70-80 range, my body started demanding calcium like never before. I was astonished. I set my magnesium at 250 mg twice a day, started in on the vitamin D, and as my blood level rose, so did my need for calcium. When I was taking very large amounts, and said "This is crazy," I set out to figure out how to reduce the calcium to more normal levels. Enter vitamin K. Bless Torntotears, he did a posting on vitamin K2, Mk-4 form, in 5-mg capsules from Carlson, plus research on its use in osteoporosis and atherosclerosis. When I took it, my calcium need started decreasing. The way I figure it, I had trouble getting the calcium to go where it needed to, and the vitamin D and vitamin K filled the bill. (I can't think about where the calcium was going before then. It's unnerving.) Your results could definitely vary on this.
Regarding your Iodoral and SSKI dance -- you may be working with a need to balance the two. I love a good amount of SSKI, but the elemental iodine in Iodoral is basic for me as well. Taking 50 mg Iodoral with 3 drops SSKI has been a good ratio overall, which I can slide up when I need to. Your ratio might be different. I don't think I'd try to fight a lung problem with less than 100 mg Iodoral and 6-7 drops SSKI, or more drops if I needed thinning of mucous.
Best wishes as you sort yourself out of these issues!