There is no such thing as a Top-20 MD/PhD program since there are only 40 or so MSTP-funded programs, and they all know each other very well. That said, yes, your metrics may be a little lower than ideal for MD/PhD consideration, but not impossible without a strong application talking about why you have prepared well for the MSTP track. Have you gone to affinity-related research conferences such as SACNAS and networked with admissions officers and recruiters?