chef,
I have also thought about some of those issues. My wife will be working full time, so once she gets a job in whatever city we move to we should be doing great financially.
Until she finds a job, however, its going to be very tight financially.
I know that the NIH DOES give out merit based scholarships, but the only ones I'm aware of are for minorities.
You could try getting some loans, I know that at Yale they specifically advise you to try to get loans becauuse the living stipend at Yale (believe its around 16k) may not be enough for New Haven.
Your best bet would probably be for a loan or a small scholarship from somewhere other than the NIH. Most of the NIH awards are pretty big (similar to MSTP size) so I doubt they would give you an MSTP grant and THEN on top of that give you another merit scholarship which comes close to the amount of the MSTP. Perhaps they do have some smaller schoarships you can apply for that I'm not aware of.
Of course, for public loans using the FAFSA, they might not give you very much money, since I think they will require you to divulge that you have been awarded an MSTP grant and they will calculate that against you in your financial need profile. So you might have to go to a private bank and get a loan at a somewhat higher interest rate.
For some locations, I think living within the MSTP stipend is entirely possible. At WashU for example, I think you can easily find apartments for only 500-600 a month. WashU is going to have a $20,500 living stipend starting this year, so that should be good enough to cover it. At other schools, however, perhaps like UCSF, the cost of living makes it very tough to live within the stipend. My point is that location matters a lot.