Creating Customized Setup

I want to create a setup program for the project (say Project 1).
But this setup is also created thru one another project (say Project 2).

Project 2 has checkboxes to select that...
which modules should be incorporated for the final Project 1

So finally the setup for installing Project 1 that gets ready thru Project 2 should contain only those modules that were checked.

is it possible... and if yes till what extent.

or suggest me the best possible way to restrict the users of the final project accessing those functionalities of the project that are not available to him. i have maintained a table Menu_Master from where all the menu items come. and that table is not editable thru the project. but what if the user replaces the database file with the one from someone who has got all the modules checked

please guide me...