Probably late to the party but not reporting your score doesn't doom you. I did not report my score (worse than yours!!) and was accepted to the only program I've heard back from so far (U of Rochester). So yeah, it's not a total loss.
I did not report my score (I was in that same boat as you) and have so far been accepted to Rochester with no other decisions in yet. Not quite the caliber of the programs you have listed, but still top 50. Strong GPA, general GRE, and research should work in your favor and can outweigh not reporting the subject test score.
Research and recommendations definitely make it possible to get in even if you don't exactly have a 4.0. I have a 3.4 and have already been accepted to a top 50 program. I will have a little over a year of research once I'm done with undergrad and one publication. Didn't think I'd be here after a C+ in Organic I .