Rollo:
While not applying gen surg, I was in a similar position as you last year. My dream is to be an orthopaedic surgeon. I knew I had the numbers/class rank/research to go MD ortho had I gone to an MD school, but I too am a DO student. There aren't any DO ortho programs around me, so my only experience was with MD residencies. I also knew that if I rotated at DO residencies that my top choices would still be allopathic.
I originally set up one DO rotation and 3 MDs; however, the DO got cancelled due to school affiliation agreements. Then, I got my step 2 scores back, and my USMLE was WAY higher than my COMLEX. I took these as signs (I prayed a lot on this), that I was supposed to go only MD. I decided to go for the gusto and only apply MD. My reasoning was that if I knew my top choices were going to be ACGME, I should put 100% of my efforts into getting into an ACGME residency. If I rotated half and half, in my mind that was putting half effort into each. Therefore, I rotated 3 MD programs. So far, I have gotten 5 interviews, 1 wait list and 15 rejections, with over 100 schools to go. (If you're gonna do this, you're gonna have to go for it - which means apply broadly)!!! So far, it's going OK, but I'll let you know how I feel come March.
If you decide to do this, I would choose at least 2 rotations with "DO friendly" residencies (i.e. either have a DO resident, have had one, or you KNOW they would take one). Go where other students in your school have gone/interviewed also. If you have a dream to be the first at one place, then go for it. There always has to be a first one! That's how ground is broken! Just know that you can't be just as good as your MD counterparts. You have to be better! However, don't do 3 rotations at 3 top 10 MD residencies that have never had a DO. That would be stupid. You have to be realistic.
Rotations will be crucial for you. You must excel.
Get ready to get a LOT of rejections. You will feel like the smelly, fat kid at the dance that no one wants to dance with. It's OK though, because maybe a hot chick will take a chance and dance with you. And when she does...you'd better be Usher or Emmit Smith from Dancing with The Stars or something.
Another crucial point - you have to be prepared to NOT match. This is possible. I understand that it's still very possible for me. My back up plan is to rotate and apply DO next year if I don't match this year. The way I look at it is...it is just one extra year of my life to have a chance at living my dream.
I am not saying this is the route for you. You have to pray about (or just think real hard about if you're an atheist) what's right for you. This is not the path for everyone, and I certainly don't recommend it for everyone. I also know nothing of the gen surg application process. I do know that the average boards scores and the percentage of people not matching are both higher in ortho; however, I've also heard that ACGME gen surg is more unfriendly to DOs than ortho. That's just hearsay, though. This is simply my point of view and some pointers should you choose to go this route. I understand this is a very stressful decision, so if you need any more advice, PM me.
I hope this helps and good luck. 🙂