Visit your OB-GYN and rule out anything physical first.
Then you should seriously consider counseling. It isn't mentioned anywhere in your post, so I am going to operate under the assumption that the "we have emotionally dealt with it, for the most part." line is you and your boyfriend and not you and a licensed therapist. You also do not say how old you are. 16 1/2? 46? 96?
Dealing with rape trauma is the kind of thing that you need to bring the big guns in for, and work with a professional. There is no shame whatsoever in getting proper treatment for an injury to your psyche - it's what you would do if your arm was broken, right?