I removed old versions of libtorrent and deluge on the system (with apt-get purge deluged deluge-common deluge libtorrent-rasterbar-dev libtorrent-rasterbar6 python-libtorrent)
And also removed all I could find under /usr/local/lib/python2.7/dist-packages/ that was related to libtorrent and deluge (that I had installed manually before).
Then I did this (I'm running a default installation of Raspbian):
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git clone -b 1.3-stable git://deluge-torrent.org/deluge.git
cd deluge/
sudo apt-get install subversion
vi get_libtorrent.sh
Change VERSION=14 to VERSION=16 and save.
python setup.py build
sudo python setup.py install
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pi@raspberrypi ~ $ deluged --version
deluged: 1.3.6-dev
libtorrent: 0.16.13.0
Now onto setting up iptables to only allow deluge to connect to Internet when VPN is up, but that should be easy...