After wrangling with this problem for some time I did find a way to control the branch referenced when using source 'your-repo'
from the podfile (not the podspec!!). Turns out that the podfile isnt actually pointing to master, but rather the "default branch" set in the github options for the repo. So if you go to:
GitHub Repo -> Settings Tab -> Branches -> branch you want -> Update
The default branch for the repo will be updated. After that you need to wipe the local cocoapods repo (it seems to cache the previous default branch name otherwise)
rm -rf ~/.cocoapods/repos/your-repo
Probably wouldnt hurt to wipe your pods directory and cache either. Anyway, after that, your next pod install will pull from the correct branch.