I've inherited a Wordpress site that uses http://podsframework.org/ CMSframework plugin. unfortunately the previous admin created so many pods, which in turn created a lot of custom post types that have now hidden all the adminmenu link like options, themes, users etc aren't displayed anymore. So how do I get them to display?
This is a known limitation by the WordPress menu functions, you would need to rekey all of the menus ahead of time to be +100 or whatever you need, before Pods adds the menus to fix this. Previous versions of WordPress had a bigger problem with this, but they recently increased it in the past year or so.
Also, in the Pods setup area, you can specify per content type, whether to show the menu item in the admin menu or not. That could help resolve some of those issues, and any content types not shown in the admin menu top-level, will be added to the "Pods" top level menu as sub menu items so you can still get to them.
Not saying this is your solution, but it may be a good place to start looking...
Wordpress has it's functions.php as I'm sure you know of. Well, I just recently added a Admin Dashboard widget through my custom theme's functions.php. The call to add it was simple enough and even if you're foreign to touching this file, you could check for the Wordpress hook names and get a good enough idea as to what they do:
Again, that is to add a Wordpress Admin Dashboard widget, mostly used to pass along important information about the theme or something found within it. Developers use them for their Plug-Ins as well from time to time. The "Your widget text here." section is surrounded by a paragraph tag, HTML can be placed there to mark it up nicely for the Front End user.
Again, not sure if that helped or if I'm totally off but I believe the logic is the same. Just need to find that hook that calls to add those side links methinks... But, I might be totally wrong. Sorry!!