Yes. You have nothing to gain by making separate installations unless you intend to use these modules in separate places. I don't really understand the problem with the unit tests. You can make as many tests as you want and they can test anything you want. I have a whole bunch of different test files in my current project, all testing different modules, and they all just sit in my t/ directory.

what is a good way to determine which version of each module is currently installed on a system?

Add a $VERSION variable to each module.

what is a good way to handle the build process so that only those modules that have been modified are rebuilt? I can do a CVS update of the module sources on each system, but I need some way to determine which modules need to be re-built and re-installed.

This is an example of why you shouldn't split these up. Your global Makefile idea would probably work though.