Their is a lot to learn about disorders in tortoises. Probably, the tortoises were ill or weakened from the beginning. Next time be very careful choosing tortoises. If an animal is sick when you get it you will have problems and deaths. Shipping a small tortoise is very stressful and perhaps caused serious injury (dehydration, overheating or lack of oxygen). Your husbandry conditions sounds adequate. You have to trust that they have the will to survive. As has been said, mixing different species has proven to spread disease. People have lost whole populations due to infection ( Herpes virus etc). If you keep enough living things you will have deaths. Living things die. In nature the majority of tortoises die before reaching adulthood. Hang in there!
I'm definitely not giving up on them....just finally got to cut the grate thing out so they have way more light coming through from the mvb. We'll see, they both seem a little better with big boy gone.