New pull request was created. This time I created a branch to work on and then merged that back to my personal master before submitting the pull request. That feels like the right way to do it.
EDIT: I found another article that explained what I should have done with my previous repo. If I fall into that issue again I will try this route…
git checkout -b {my_pull_request_feature_branch} upstream/master
git cherry-pick {sha1_of_first_commit_for_feature_X} [sha1_of_another_commit_for_feature_X] …
git push origin {my_pull_request_feature_branch}
from: http://stackoverflow.com/questions/16984169/github-how-to-submit-individual-pull-request-in-case-of-multiple-commits