First of all, forget about it, you can't change it, and focus on what's ahead.
I was in the same boat after step 1, took step 2 in July of my 4th year and focused on my clinical rotations and away electives. I don't know what others will have to say, but I would recommend taking step 2 ASAP in your schedule and having it in your application. I can't imagine many programs would wait for pending step 2 scores from an applicant who "choked" on step 1. They have plenty of applicants that didn't and they don't need to wait for you. A strong step 2 staring at them may help them overlook your step 1.
There are some programs that don't look at step 2 even if you have it in your application, so you aren't going to be interviewing at those unless you rotate with them and blow them away. I ran into this exact situation at one of my aways and was told flat out that I would not have been offered an interview if I hadn't rotated because my step 1 fell below their cutoff. My step 2 was above their cutoff, but I was told they don't have the time to deal with that and just make their cuts on step 1. Don't know if I actually made it into a position to match, but I did get an interview at a top notch program without the typical scores.
How far below the national mean you are will obviously affect your application, but taking and rocking step 2 can only help. You still want to submit your application as soon as possible and have your scores in as soon as possible.
Hope this helped and good luck. If you want ortho, it can still be done.
