This post was originally about xkb symbols, but I altered the title to fit the solution I found. I followed the instructions on
http://madduck.net/docs/extending-xkb/
to modify my keyboard map, which unlike xmodmap actually works.
xkbcomp $DISPLAY xkb.dump
edit xkb.dump to fit the new layout
(In my case I swapped the Ctrl and Win keys)
xkbcomp xkb.dump.modified $DISPLAY (may be necessary to run this twice)
log out and back in
To preserve this across a reboot, I created a file $HOME/.config/lxsession/Lubuntu/autostart (again, many thanks to the Archwiki people), which reads
@xkbcomp xkb.dump.modified $DISPLAY
