“osx-app.sh” is a srcipt I wrote to automate building the Pd .app bundle. The -i option tells it to use the included version of the Tk 8.4 Wish.app. I think that may work for you, so that set of commands tells you how to try building manually. The “make app” command runs this script but uses the latest Tk on you system which may not be fully working yet.
(I have another branch where I’m ironing out the new Tk issues on OSX).
The main thing is, you need to change directory in the pure-data/mac directory inside the pure-data folder.