Putting the Wii on Video 5 with analog audio will require you to connect the audio to the front panel input. I doubt you want that. I'd swap the Wii and the HD-DVD player on your list above.
Also, another reason to run the Wii through the 990's component switching and then feed the 990's component monitor output to the matrix switcher: the Wii's AV cable is a single entity, and you'd need to split it apart enough to run the component video portions to the matrix switcher and the audio portions to the 990. Taking the whole thing to the 990 (assuming you take the audio to a rear panel input) will be simpler in this regard, as well as simplifying access to the 990's menu.