I’m still not clear what you see for item 3? You can write direct Python scripts and run them from the command line. This is the more traditional way of running them. If you need to run a script within the notebooks, you can use %run magics in the notebook or use %bash or ! to call out to the command line from within the notbeook. %run offers more options and better integration back into Jupyter. JupyterHub, which MyBinder is a glorified version of, includes access to the terminal and so you can run command line things there.
In regards to migrating your Mac to Python 3, I understand. However, thanks to MyBinder and other places I can leave my local computer alone and run Python 3 remotely. That has allowed me to not mess around with my working local system but explore Python 3 a lot more easily.
I’m familiar with Shiny. For converting a Jupyter notebook to an application you can use appmode or Voila. This recent answer might help you understand those better. Both can run on remote sessions served via MyBinder so that you can test the basics there.
For PMML, there is sklearn2pmml or Nyoka; see here for announcement of Nyoka replacing py2pmml. #7 here discusses various ways. Or see here.