I need to update this, to fix some of these problems. I've been doing lots of overtime at work a lately, but I should get a chance next week.
The Pandora key doesn't toggle the menu because, to do so, I'd have to modify the source of Openbox itself. I'm not a programmer, so it's not normally the kind of thing I look into. I did look at it recently though, and I'm fairly sure I know how to change it so that: 1) the menu closes with a second press of the Pandora key, and 2) it opens at a fixed position, without moving your mouse cursor.
The system menu is normally there (including SysInfo). If it's missing, it's because of a non-standard PND breaking the menu (as mentioned, the Codec Pack is the main offender, but there may be others).
Program categories can't be in the root menu, because they're generated dynamically (e.g. if you don't have any Office software, there's no Office category). To update the root menu, you have to change menu.xml, and then run '/usr/bin/openbox --reconfigure' (which isn't something you want to do every time a new PND is added).
The "Toggle Tint2 Panel" and "Toggle Warlock Bar" are intended to be temporary: i.e. they're something you have running, but kill off when you want the screen space. If you always want them disabled, use Root Menu -> Openbox Config -> edit autostart, and comment out the relevant entries.
Anyways .. now I must sleep ...