WireDesignz HMVC might be useful for you. You can keep all your separate apps in different folders (each with their own views and controllers).
Your 'main' app would just have to deal with permission to access, and calling the separate controllers within the HMVC framework.
Will make testing much easier, keep separation for your apps and it is very robust once you get the hang of it. Building an app like this on the back of a codecanyon example is not a great idea, should definitely be doing this from scratch.
You should also move the settings for each module into their own tables. Much easier to control that way. So module 'projects' reads 'project settings' from a projects_settings table. Much cleaner.
My only advice from a job perspective is to be careful. Your desire for clean lovely code for good reasons may not be shared by your company if they already have code that works. They may be much more along the lines of 'if it aint broke dont fix it', rather than taking the full brunt of the blame for every limitation, bug or issue that arises in the future. Working with the disastrous code at least protects you from the point of view that 'its not your fault, it was how the code was designed in the first place'. And they may not be in a position to wait months and months for your version to come up to production level.
Of course I do not know what your remit or job description is, but a plan moving forward might be to work on both, the live stuff with support, bug fixes and improvements, whilst developing the new version when time allows. It sounds to me like your company was never into making beautiful code if all this is a revelation to them. And your direct report, who is currently understanding and listening, may be saying all sorts of things behind closed doors with her boss.
Good luck,
Paul.
