Dr2B2009,
I'm a first year MD/PhD student at BU so I can answer some of your questions. In terms of funding, BUSM gives partial funding for MS I and II years (they pay for the difference between MD and grad tuition so you pay the grad tuition amount). Lab rotation is not required pre-MS I summer, but you have to do rotations during summer between MS I and II to get part of the MSII funding. Then it's full funding with stipends during your grad years. For MS III and IV it's ~$22,000/year I think, but it could be more or less depending on your grad/clinical situation.
As for research there are many opportunities available. I am interested in neuroscience research and that's available in just about every department here. The Biosquare will bring in many biotech companies/new laboratories so that'll be a plus in the near future. You see a very diverse patient population at BMC as you may already know.
The program, although not fully funded, is has a lot of potential. We just got a new MD/PhD program coordinator who is looking forward to bring better integrations to the program. He is very willing to listen to students' opinions. I am very happy so far and am in the beginning stage of looking for a lab for this summer.
From what I know, the program does allow MD only students to apply during their first or second year. You should contact the program for more info. Hope this helps and feel free to PM me if you have more questions.