I graduated from undergrad in 3 years, and my advice would be that unless there's a specific reason why you want to stick around for the MS (e.g., there's a PI there that you'd really like to work with and he/she won't hire you but will take you as a masters student), just graduate and get a full-time reasearch position.
The only caveat with that... make sure the PI that you'd be working for understands that you want to matriculate in a MD/PhD, that you will work hard and do whatever you need to in terms of your research project, but you'd appreciate the acknowledgement of projects completed. Surprisingly, quite a few PIs have a policy of not publishing ppl who are on payroll. Not that you can't get into great programs w/o publications, but if you've done the work, you should get the credit.