Through a little experimentation, some advice from the vast and friendly internet, and a genius suggestion from Bryan Young I have been able to automate the conversion from the flash outlined characters to a pencil-like look. I was previously planning to perform this process manually by tracing everything, though I soon realized such an attempt would render me a weeping shell of a human discovered by some lonesome vagrant rifling through a local dumpster. So instead I have saved myself from such a fate by using After Effects to complete the task for me. The results are not perfect, but are pretty close to what I was looking for. Here are a few examples.
Final Look - Paper Characters from Michael Spilsbury on Vimeo.