Grifmet,
Here is a handy Cyclosporine guidebook. It was written for another autoimmune condition but is a very thorough source of information on dosage and side effects. Note that it recommends that trough measurement be between 50-200ug/L. Hopefully, they lowered her dosage considerably. 580 is too high for a trough.
http://www.argbc.ca/files/Cyclospori...Physicians.pdf
Dana Farber is a recognized MDS center of Excellence. So, in that respect, it could be a better choice over Yale.
As triumph said, life is so much easier when you have a doctor that is an expert in the field. I wouldn't go back to her current one.
With regards to magnesium...it took a few years for my deficiency to show up. Everyone is different and as long as they are monitoring her, there is no need to worry. Make sure she avoids grapefruit. That is a known restriction for her diet!