So I started playing with my hotkeys today, and much to my dismay, I seem to have irreversibly set the delete hotkey. This is extremely annoying now because instead of deleting the selected text, it executes the command that I put in. The problem is that that specific command is not listed under system>preferences>keyboard shortcuts. Somehow I set it to open the terminal, and now I can't turn it off. (One thing to note, though, is that I can set another command to do nothing with delete as the hotkey. Then terminal doesn't open, but I still can't use the key!)

That tool can be a bit of a nightmare. Instead, go to Applications menu and run System Tools - Configuration Editor.

Click on apps - metacity - global_keybindings. There you can change the setting for run_command_terminal by typing in the name of the shortcut rather than just pressing keys; e.g. I use <Super>t, which means Windows flag key with "t".

Not being able to use a key sounds like you've altered one of the shortcuts that use buttons (like XF86Mail) by default. That's fatal! I tried replacing XF86Calculator with <Super>c, and disabled "c". Use the Configuration editor, clicking on apps - gnome_settings_daemon - keybindings and make sure that no shortcuts are defined there except those using XF86 buttons.

Back in apps - metacity - global_keybindings you'll find entries like run_command_1. You can use these to add your own key bindings and then define the command in apps - metacity - keybinding_commands. e.g.
run_command_1 <Super>c
command_1 gcalctool