We finished doing an initial remediation on a site infected with SUPEE-5344 (See previous article). We built a script that we tuned to try and find files infected with our particular variant of this nasty bug. We are providing it (without support/warranty) to the rest of the eCommerce world in the hopes it may help some folks clean their shop.
We highly recommend that folks get a web application firewall like Incapsula or Cloudways nowadays. Its not fool-proof, but it can help mitigate some of these exploits before they begin.