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My solution, albeit probably not the best one, was to do away with the main menu altogether and make two new ones using custom blocks. I just wrapped them from html into the block, used my theme's CSS for consistency, and it worked out fine. Now, when I want to add a new menu item, I just edit my html file, put the item where I want it, and copy it to my custom block for that menu area.
I have four blocks now, just using one of the old ones as a template when I make a new one. Like I said, maybe not the most elegant way, but very effective for me.