I notice you add the new levels in chapter 5. The newest release of World of Goo supports booting a level from the commandline (excecutable [Levelname]). This makes sure that you don't get extra balls on your profile*, which you would get if you add them to chapter 5. (Yes, I think that's important, because I have the most balls

)
I've done some work with this and decided that the command line option is definitely for developers only. (In fact it's largely superfluous, since most times you can just "reload" level and it'll re-read the level files fine, you only need to restart if you edit text.xml)
First off, it loses the level title/subtitle and just replaces it with the directory name and "testing 1 2 3". Fine for developers. It can't know the real title/subtitle because the text lookup key for this is actually in the island.xml, and you're bypassing the island. Not something I'd think would be easy to fix.
Second, you can't have OCD requirements because again they're stored in the island.xml (in fact you get a crash if you try to access the OCD menu option).
Third, you don't seem to be able to play *new* level names via this mechanism, though I'm making a separate post to try and track down why this is.
And finally, it does mean you have to go through the game startup sequence every time you want to launch a level from the tool.
So I'm going to go back to having GooTool add levels to chapter 5, and when WoG has support for more chapters, move them to a new "custom levels" chapter.
As far as balls on your profile go, I imagine they're calculated as the sum of all balls in all levels you have completed, since it's not actually stored anywhere on your profile. As long as 2dboy code only looks at official level names when totalling, you should be fine.
David