OP, your big hurdle is going to be your rape charge. I have an arrest but no conviction and I can tell you what I learned from my case. Here are your big hurdles (coming from a non-lawyer)
1) Getting into medical school
Half of the schools I applied to this cycle ask for convictions and charges. I think you're going to be DOA at schools that ask for charges. For DO schools, background checks are not run until after an acceptance has been offered. I did not apply MD but I have heard that AMCAS will run a background check and attach that background check to your primary applications. This means that without an expungement, all MD schools will see your rape charge. DO schools will only see your rape charge after they have accepted you BUT the handbook I read from my DO school says that they can pull an acceptance if they find anything in your background that would prevent you from completing your clinical years. I'm not sure if a rape charge would prevent you from rotating but a school could still use that as a reason to pull an acceptance. In Florida, medical schools are not entitled to view expunged records so I highly suggest getting your charge expunged before applying. In Florida, it is fairly easy to expunge a charge that did not result in a guilt plea or no contest plea but you should check your state's laws to see if you can get your case expunged.
2) Completing rotations
Every hospital you rotate at during your 3rd and 4th years are going to run a background check or request a copy of your background check from your school. As of now, every hospital will see your rape charge and could deny you from rotating at their hospital. Florida is the only state I know of that requires disclosure of expunged records for clinical employment. Every other state I know of does not release expunged records for clinical employment, meaning most hospitals would complete a third party background check. Government hospitals can view expunged records so rotating at a VA hospital will require disclosure of expunged records. I called my local VA hospital and talked to their HR person in charge of running background checks. He said they only consider the charges and they do not take into account convictions. He said they look closely at charges less than 36 months old but after that, it's not a big deal. My charge was a juvenile 2nd degree weapons felony and he said it was no big deal. You should call your VA hospital and ask if your charge would disqualify you from rotating. The VA seems to be the strictest in terms of rotation sites so I imagine if they say you're good, most other hospitals would say the same.
3) Getting Licensed
In Florida, the only entities that can successfully petition to view an expunged record are government agencies (the department of health) and employment that involves working with children. My attorney told me that medical schools do not fall under any of those categories but he said that I would have to disclosure my arrest when applying for my license. I called the Florida office of Physician licensing and the lady told me my case would not prevent me from getting licensed. All I said was expunged juvenile felony (I didn't even mention what the charge was for) and she said I will be fine. You should probably call your states licensing board and ask about your charge/case.
4) DEA license
The DEA has a list of possible disqualifications for licensing on their website. I can't remember exactly but I think all of the disqualifications were drug related/domestic violence/ felony drug convictions. You might want to also call their office and ask.
I think the key here is getting your case expunged. Getting an expungement will avoid schools from seeing your charge and then rescinding an acceptance because of it. I would avoid schools that ask for charges as it could be problematic if they find out about your expunged charge during rotations.
Again, I'm not an attorney BUT I did talk to two attorneys (one being a criminal attorney I spoke with on the phone and the other being my old criminal attorney from my juvenile case) before applying and I read all of the Florida statutes on expungment and physician licensure.
