As a student who has gone through this process and run a revisit weekend or two, here are my two cents. I wrote this in an email for a friend who was revisiting for MD-PhD, I see your second look is run by the grad school only. I would try to focus on MD-PhD students in particular, as their experience can be quite different than the grad students, and I've attached my MD-PhD rather than PhD specific advice below if it helps:
Talk to some older students (ideally have done lab and clinical stuff), see if they're happy, what they plan on doing with their careers. Can you imagine yourself in their shoes?
Ask the PD for average graduation numbers and match lists (with less emphasis on prestige and more on who actually ends up going into academic medicine, for example, are they all matching into medicine? neurosurgery? family practice?), see where their students end up and how long it takes for them to do it.
Ask about housing, living in that city, what there is to do, etc. Can you afford to live there on a stipend? See if you can visit a house or two, are students stuck in crappy little one bedroom closets, do they know their way around the city, where to have a good time?
Look at the interaction between students and their research mentors. Is the environment casual, can you knock on someone's door and expect to chat or will they say "go away, I'm busy." Don't rely on this too much, you might just catch someone on a bad day and all PI's are busy, but see if you can get a gut feel.
Finally, look at the MD-PhD program itself. Do the students hang out with other MD-PhDs, other med students, grad students, everyone, etc. Does the program director take his responsibility seriously, can you knock on his door if you have problems? Does the program seem well-run, are the administrative assistants pleasant and seem on top of stuff?
You take all that information and combine it with the schools research reputation in your field(s) of interest and reputation for clinical training, and voila, you have a good basis for picking a school. Most MD-PhD programs are good, and ultimately your happiness will have more to do with your own traits and luck than the institution, so don't stress out too much about this decision and just try to gauge where you feel comfortable.
