I am in a similar situation except that I did well on the stepI. I have okay clinical grades and average basic science grades. I talked to my ortho chairman, other ortho faculty, and the dean. They all said that despite the slightly above average grades (at best), I still had a good chance of matching. Luckily, I have good research experience.
Like you, I did well on my ortho away rotations. so my advice to you is to ROCK on your away rotations and be smart about where you do your aways. That may make a big difference. You should also talk to your ortho chariman and your dean.
I also wonder how much weight programs give to applicants' medical schools since it is probably easier to be AOA at a less competitive med school than in a med school that takes mostly aspiring Einsteins.

Good luck with the process orthorun.

If your grades in the first two years are average, your third year grades are average, and your board scores are below average; you are in a difficult position. An exceptional orthopaedic rotation will only help you in one program not all the ones that you should be applying to. 1) Quickly get involved in research. 2) Take part 2 of the boards and rock them. 3) Make a set of contingency plans if things don't work out.