If it were my stuff I might write a Template for the Makefile.PL and use a prompt module (or something handrolled) to ask, "include this? (y/n)" etc and take the results of the prompts to write the final Makefile.PL. I think Module::Install might even let you do a lot of that inline if you just wanted a big single one. Makefiles are just Perl scripts after all. The script (or I'd just as soon do most in the template in a case like this with THROW and such) would keep the logic for interdependencies, etc.
Come to think of it, TT is probably a poor choice because it might not be installed on the target machine; but you would probably be generating dists on your box... anyway, you get the idea.
Then you'd also need to use the information to decide which tests to run on the given installation. You're running all the wonderful tests you've spent the years amassing, right? :)