they are all tiny scripts, as the bulk of it lies in modules.

Coolness! For something like that, yes, CGI::Application makes a great deal of sense. Since you've already done most of the refactoring work, you should have a win with using runmodes over a hand-rolled calling solution, in the long run.

Plus, it makes it easier to pass auth or other data, which can help tie your application together. That's a win, and I think your instincts are dead on.