EDIT: Works for root, sudo is the problem. Read below.
I have a directory with my own libraries, e.g. my Python libraries are located at /home/name/lib/py
The same is true for the PATH variable, it's also not carried into the super user environment, even though you're passing the preserve environment flag -E.
I'm using this sudo command now without any other modifications:
sudo -HE env PATH=$PATH PYTHONPATH=$PYTHONPATH ./bin/myscript
Since it's an alternative approach that works (for me) I thought I'd share here.