Hi, I’m not sure I got your workflow.
Eyesy won’t start at startup and running ~/Eyesy/start_web.sh via SSH will give no result in the terminal or on the Pi desktop, it’ll only start the web editor.
Then with both the RasPi and another computer (or your phone) connected to the the same network, use a browser (not the RasPi) to go to http://raspberrypi.local:8080 or [your RasPi IP]:8080
Then click on “Start Python” and Eyesy should start.
“Start ofLua” won’t work, so focus on Python for now 
About Midi over USB, try to modify amidiauto as explained here → Patchbox and ORAC - #11 by Giedrius
Just to be sure, are the CC set correctly on the MPK?