Since you have hypothyroidism, I would suggest starting and probably staying with 6 days a week. Short and intense should be your goal, this will increase your metabolism.
I started nice and slow. Sounds like this will be good for you. I just did one set of everything. I did heavy as I could for 8 reps. It will take a few sessions to figure that out, of course.
Eventually this didn't kill me, so I would add 15 minutes of cardio. Since you are "VERY" out of shape, this will just help with your stamina.
Eventually this didn't kill me either, and I'd add another set of everything.
I would suggest
Upper Body on one day. Lower the next. 3 times per week.
ACHY - you don't really describe this in detail. Anti-oxidants. I take these just after I workout. I am much less sore taking these.
Essential Fatty Acids, these work great for me. If it's joint pain, Glucosamine works well. I would not take an anti-inflammatory before you work out (tylenol etc.) This blocks cortisol to some extent, and has made my joints achier.
Massage - people often "learn" to carry themselves the wrong way. This eventually just makes everything hurt. Deep tissue massage can help. Luckily it's kind of painful.
Hope that helps.