I found a fix, Put the Servergrid.json into the editor and save it, this fixes the islands, but the npcs wont spawn, the fix for this, (at least for me) was leaving the zone and dieing, then respawning at the free port and they were all back.
there seems to be a problem with the 1.3 version of the map, every single island except powerstone islands and freeports are floating with no land what so ever but resources are there is there a fix to this?