How did you make the SVG? I assume you used Inkscape? I have a thought... If you used the rectangle tool, and just duplicated the rectangle over and over, may I suggest turning on "snap to cusp nodes" on the toolbar along the right side of the interface? Then, drag the squares into the approximate location, and it should snap and read "corner to corner". If you snap each rectangle to the next, all the squares will be perfectly aligned, and not slightly off-centre as they are now. You can then just save the SVG and re-upload it. As long as you don't change the "territory_id" #s, you wont have to redo any of the centrepoints, names, bonuses, connections, distribution modes, etc. It will all be copied over. Although, because you used regular shapes such as rectangles in your map, you may find it helpful to use Matma Rex's automated centrepoint tool: http://warlight.net/Forum/Thread.aspx?ThreadID=2452
. This will put the centrepoints exactly in the middle of the territories.
You aren't required to do any of the things I suggested, but I do feel that the map would be more aesthetically pleasing if you fixed the mentioned things.