I think you should try to send in applications to schools that don't require the subject test at all, and/or schools that don't make it a compulsory aspect of the application. This will better your chances (unless of course, maybe you already sent scores using the free score reporting option). That's my plan, at least, if my scores aren't too good, because I am in similar shoes, but a little more optimistic. Hoping hard for up to the 60th-70th percentile.
I don't feel the GRE subject test is a fair assessment of my ability to do research because my only interests in Applied Math are in calculus related research (along the lines of numerical simulation, finite element PDE solvers etc). I am from an Engineering background and didn't see a reason to study some extraneous topics in Math, which I am meeting for the first time and will probably never meet again in my career. Welp. I'll probably pay for such folly with my scores.