First, good job on the list, looks like it took a lot of work. It's a good way to gauge an institution's powerhouse-ness.
However, I think there are many other metrics that would be more useful to comparing MSTPs, such as the size of the T32 training grant, the size of the cohort (bigger programs tend to be more successful), average number of first author publications per student, average program duration, % of students completing the program, etc. I know you don't have this data, but I'm sure someone does. I bet the guys in the NIGMS section that reviews MSTPs have all the goodies, but they won't spill the beans.
Also, now I get to go on my rant on how I don't trust the total NIH funding spread over all "affiliates," particularly Harvard. I've always thought the way Harvard takes the credit for all their affiliated hospital's research is... sketchy, to say the least. I mean, does Harvard actually hire/fire and pay the salaries of the people who work in MGH, BWH, or Deaconess? The total funding in 2013 for all Harvard affiliates is some ridiculous number like 1.3 billion. But if you add up just Harvard college + HMS + HS-Public Health, you get ~$350M, which is still a lot, but nowhere close to Hopkins or UCSF. Besides, what counts as "affiliate" anyway? I mean, UWashington is "affiliated" with Fred Hutchinson Cancer Center, but I don't think it takes credit for the research there. Same with UCLA and Cedars-Sinai Hospital, or Stony Brook and Cold Spring Harbor. An institution like Hopkins puts its name on every one of its hospitals ("Sidney Kimmel Cancer Center at Johns Hopkins), so there's no confusion there. In the end, it's all very tiring and I like to pretend the numbers don't matter. ¯\_(ツ)_/¯