That looks like... an undertaking. And pretty impressive so far, at that. I recommend that you do not overlap bonus borders-make them adjacent to each other. Helps people when playing the game to not have to check the bonus button all of the time.
Also, I recommend that your city bonus links be a different shape so that people do not get confused by them.
What do you mean, non overlapping borders? Of territories, or of bonuses? For bonuses, I do it by moving each node. I use drawsvg.org (I don't have access to Inkscape) and so I can't do the easier way, but I've realized that if set the border radius to 20px and then make the borders barely touch, it makes decent double borders. For territories, I also move each node, but some overlap is fine, as it doesn't(shouldn't) show on the map.
Yeah.... I only realized this after playing a game on the mobile version, so from now on, I'll try to make every territory without noticeable overlap. Might go back and make a mobile version as the next version of this map.