So let me understand this...

you have 200+ pages, and they're all different depending on what type of user permission you have? Shouldn't the page dynamically address that? Or a menu on the left side of a page address it?

The menu removes or adds buttons based on a user's group or user permission...

Or the content area changes depending on the group or user permission?

"What I'm looking for is an idea or tried and tested way to build serveral web application that work together and will publish to the same root directory."

Web applications can make http requests to one another (webservices model).

But if you want to have 4 projects, and have them all publish to the same directory... and operate as one... I don't think maintaining that would be wished upon your worst enemy. They would have to exist in seperate directories under a parent directory.. and already I would be at a loss to figure out errors..