Nice write up. However, I'd recommend acouple of things:
1) Use /home/user/.config/menus/hildon.menu for your custom menu
2) Use /home/user/.local/share/applications/hildon as the dierctory for your new menuname.directory files.

It should be safer than editing the files you mentioned, and your new menu structure will persist if you have to reflash.

3) Some appname.desktop files already have categories listed and may show up in unwanted places. If this happens you can use <Exclude> </Exclude> tags.

There is some good info in a ouple of threads:
Making and managing folders
apmefo thread.

Apmefo is also very good dor beginners as it modifies all the files for you. Catagorize and MyMenu offer some automatic categorization.

But a very nice write up nonetheless.