You already have one significant weakness in your app, so my general advice is to make the rest of your app as strong as possible.
First, you will want to do well in your PhD, especially assuming that you plan to apply to research-oriented residency programs. Make sure that you and your PI are on the same page concerning your graduate program. Check in regularly with him/her and with your committee members so that there aren't any "surprises" when it comes time to defend.
Second, spend some time in clinic if you can. I know you haven't done rotations yet, but see if you can at least get a feel for whether you want to do a surgical versus nonsurgical specialty. This will allow you to do some networking with faculty in that area like nothingman suggested.
Third, when you hit the wards for third year, you need to honor as many rotations as you possibly can, and *especially* the rotations in whatever specialty you want to enter. Find out ahead of time how your school grades clinical rotations. Some schools put a lot of emphasis on shelf exams, while others care more about clinical performance. You need to know what your school does so that you can expend your time and energy in the most productive way.
Fourth, as nothingman said, take both parts of Step 2 early, but only after you have done some serious self-reflection about what went wrong during your Step 1 attempts. For Step 2CK, make sure you take several practice exams, and do not take the real test until you are sure that you can pass it on the first attempt. The good news is that most people do better on CK than they do on Step 1. But for you more than most people, a strong showing on CK is essential. You also need to prepare for the OSCE portion of Step 2 (Step 2CS) to ensure that you pass that on the first try. It's not a hard test, but you will want to read over the rules and some sample cases before you take it.
Fifth, your school may require you to do one or more acting internships during your fourth year of med school. Even if they don't require any AIs, you should still do at least one. This will give you a chance to show off your clinical skills and to take on more responsibility than what you do as a third year student. Again, you will want to find out ahead of time what the grading system is for your AI so that you can apportion your time appropriately to maximize your chances of getting an Honors grade.
Sixth, when it comes time to apply, make sure that you have a good mentor to walk you through the process. Ideally, this will be someone in your own specialty. The dept. chairman or PD of the residency program at your school can be a good choice, as can a junior faculty who recently went through the process themselves. Try to get a mentor of each type if you can. The advantage of choosing a more senior person is that they are likely to have connections and be able to make calls on your behalf. The good thing about a more junior faculty is that they're in a better position to advise you on the nuts and bolts of actually applying.
Finally, you are not the first MD/PhD student this has happened to, and you won't be the last. Most people who fail Step 1 are reluctant to talk about it with their close associates, let alone post it on SDN for the whole world to read. While multiple Step 1 attempts are not a great thing to have on your record, it's not going to automatically sink any hopes you ever had of gaining a residency spot, either. Try to use this setback as a learning experience that will help you perform better in the future. The most important thing is for you to do well from now on, so that your Step 1 experience is a performance aberration and not a pattern.
Hope this helps, and best of luck.
