Doh! I just realized I'd forgotten to write back on this subject. It's actually a piece of cake. Thanks Sundance for sending me down the right path.
1. Decide where you want everything and write it out on a piece of paper. The reason for this is that the third item in your list will be the default menu selection, so you may have move several elements around. At least for me, this made things easier.
2. Browse to the skin's directory and open the "includes.xml" file. If you're using Windows 7, it's in "C:\Users\[USERNAME]\AppData\Roaming\XBMC\addons\skin.aeonmq.3\720p\." In the "includes.xml" file, you're interested in two sections: "Home Dharma/Eden Menu" and "Home Menu". The first section has the main entries like Movies, Music, etc. The second has the custom stuff in it like Favorites X, Add-ons X, etc.
3. In the "Home Menu" section, find the object you want to move and cut everything between the <item id="??"></item> tags. In the case of the "Favorites 1" menu option, that would be:
Code:
<item id="31"><!-- custom favourite 1 -->
<label fallback="31021">$INFO[Skin.String(CustomFavourite1_Label)]</label>
<include>Favourite1Backdrop</include>
<thumb>$INFO[Skin.String(CustomFavourite1_Background)]</thumb>
<onclick>$INFO[Skin.String(CustomFavourite1_path)]</onclick>
<visible>SubString(Skin.String(DisableFavourite1),true)</visible>
</item>
4. Go back up to the "Home Dharma/Eden Menu" section. There are two subsections in here, one for Dharma and one for Eden, so make sure you're editing the correct one. I'm using Eden. You'll see a list of objects in there that corresponde to the menu selections on the nav bar. Simply paste your cut text where you want it to go in that list. I'll post this section of my edited file here. My system has "Favorite 1" as the default selection, with "Settings" and "Shutdown" to the left.
Code:
<include name="homemenu_edenmode">
<item id="9"><!-- settings -->
<label fallback="31006">$INFO[Skin.String(CustomSettings_Label)]</label>
<include>SettingBackdrop</include>
<onclick>ActivateWindow(settings)</onclick>
<visible>!SubString(Skin.String(DisableSettings),true)</visible>
</item>
<item id="22"><!-- shutdown -->
<label fallback="31009">$INFO[Skin.String(CustomShutdown_Label)]</label>
<include>ShutDownBackdrop</include>
<onclick>Shutdown()</onclick>
<visible>!SubString(Skin.String(DisableShutdown),true)</visible>
</item>
<item id="31"><!-- custom favourite 1 -->
<label fallback="31021">$INFO[Skin.String(CustomFavourite1_Label)]</label>
<include>Favourite1Backdrop</include>
<thumb>$INFO[Skin.String(CustomFavourite1_Background)]</thumb>
<onclick>$INFO[Skin.String(CustomFavourite1_path)]</onclick>
<visible>SubString(Skin.String(DisableFavourite1),true)</visible>
</item>
<item id="32"><!-- custom favourite 2 -->
<label fallback="31022">$INFO[Skin.String(CustomFavourite2_Label)]</label>
<include>Favourite2Backdrop</include>
<thumb>$INFO[Skin.String(CustomFavourite2_Background)]</thumb>
<onclick>$INFO[Skin.String(CustomFavourite2_path)]</onclick>
<onclick>Skin.SetString(customFavouriteWindow,Favourite2_Background)</onclick>
<visible>SubString(Skin.String(DisableFavourite2),true)</visible>
</item>
Hope this is enough to get you going in the right direction.