Not a solution for your problem, just some comments:
After loading a flightplan foobar.pln, the directory PF3/Flight/FPP/ will contain a file named foobar.json, which you can view e.g. on http://geojson.io
It contains the sector/center boundaries used in your flight plan, so you can see how they match the real world (or not).
PF3/Data/CenterSectors.dat contains a CSV list of sector/center boundaries. This file is the only source PF3 currently uses. If you change it, make sure to make backups, because subsequent upgrades of PF3 will overwrite it.
Maybe you can adjust it for your region and provide the changes here, so Dave can include them in the next PF3 update?