Well, turned out to be more complicated for some zones, at least for removing object placements.
For now though, a quick and dirty tool:
https://dl.dropboxusercontent.com/u/...ct%20Mover.zip
Should be able to change coordinates for objects in any s3d-based zone. The remove option will be greyed out for zones where things are more complicated, for now. Haven't confirmed that edited files still work right in game but I think it should be fine. I recommend backing up any files before editing them, though.
Haven't put the code up anywhere but it's all just scripts except for the exe, which is just a shell that loads the script interpreter and gui library before handing off to them entirely.
Let me know if there's issues.