More info: Anything you save with this mod, is loaded in the mod. So you can't hax up your food and songs and then go back to the normal game; which is a good thing.
I've found that not everything works in the mod version. For example I can't click on the mural in the song cave of the door and the singers. I'm sure in the normal game you can click on it and it shows the real door and Naija giggles. So there must be some things missing. Looking for them now.
I've gotten it to start in the right map so thats a start.

[EDIT]
Ok, made plenty of progress.

I decided to take a minimalist approach and include each thing one by one untill I had a working mod. That way no unnecessary files like music would be included since the mod can load them from the main game. I discovered that you only really need 6 things in your mod folder, as well as the mod defining xml file in _mods of course:
You need the maps and tilesets folders from C:\Program Files\Aquaria\data;
You need all the scripts from C:\Program Files\Aquaria\scripts\maps, in a folder called "scripts" (it doesn't work if they're in a sub-folder, so you have to move them to the 'scripts' root folder for them to work);
You need a mod-init.lua that points to the right map, for us its 'naijacave';
You need a full entitygroups.txt, which can be found in C:\Program Files\Aquaria\scripts\entities;
And a mod icon is nice too.
With this, as far as I can tell, the main game runs just fine as a mod

(although it being a mod you can't look at the world map, could be a difficulty there

).
I've tested that nodes work, and you can place entities just fine so as far as modding the native content it looks all good; unless someone finds something else that causes the game to crash.

Now you can actually copy and put together all that stuff if you want, or its a 2.2MB download if you want my setup that should work as expected. I'm gonna make a new topic for the Copy of Native mod so that'll be where to look.
[EDIT]
link:
http://www.bit-blot.com/forum/index.php?topic=1423.0