Hey! We see the same difficulty of setting up MIDI software connections over and over again, so we’ve come up with a tiny program running in the background which we haven’t announced yet, but will do that soon 
What it does is it sits in the background, waiting for MIDI software / hardware ports to appear in the system, then it automatically connects the very first Input / Output pair of software and hardware ports together.
Anyway, I think your scenario is perfect to give it a try, you can find the code here: https://github.com/BlokasLabs/amidiauto
To install (you may have to first install libasound2-dev via apt-get):
git clone https://github.com/BlokasLabs/amidiauto
cd amidiauto
make
sudo make install
Then to get it started automatically, add to the script you use to start PD, above puredata line:
amidiauto &
(the & makes it run in the background)