1. I believe there is a conflict between the menu and the membership plugin I am using (Digital Access Pass or DAP). The sub-menu items have a lot of extra padding around them and all the navigation titles float right. This results in the menu taking up a lot of extra space.
I forwarded this on to the designers, and this is the response I got:
It's definitely a third party conflict. Something in that extension is adding css. It's probably putting calls on all A tags or SPANs, which is a horrible way to write css for an extension.
I can't figure out the exact css that's causing this, but he can try forcing it back with the following:
That would get it pretty close to being back to normal.
2. I am unable to get icons to show in the menu. I have set icons and can see them in their respective galleries, but they don't appear on the menu, and neither does their alt text.
What do you mean by "in their galleries"? Menu icons can only be assigned in the menu editor under the Flex options for each individual item (You may have to enable "Description" on the "Screen Options" tab in the top-right corner of the menu editor before you can see the Flex options), so if you're trying to add them elsewhere, that's why they're not showing up.
3. I can't get the child items to group correctly. My content is divided up into "Basic", "Intermediate", and "Advanced" levels, so I would like these menu items grouped together. Then I would like the "Basic" to have a child item grouped with three articles. I have attached pictures of what I'm currently seeing in and what I'm trying to do. I turned off the conflicting plugin for the screen shot to make the picture easier to understand.
The only screenshot you posted seems to be from a Joomla site; if it's not, and the site works exactly the way you want when the plugin is disabled, then the problem is caused by the plugin altering the menu output, which is necessary for Flex to work correctly and cannot be changed without completely rewriting the menu system.
You may find that the menu grouping you're having trouble with will make more sense once you enable the Flex options as mentioned above. It's likely that you just don't have things indented/assigned correctly in the menu editor and can fix it with some minor tweaks to the positioning of items.