Feel free to cite situations and war stories where weird practices have worked for you once.
Let me just suggest that most of your problems you've shown here are not of the grand scale of highly complex systems interacting weirdly.
Your problems are because you introduce and keep unnecessary complexity instead of removing it. If you removed stuff instead of adding more, that would help you to spot your problems faster, or at least it would help us to help you in an easier way.
But again, the stories you tell do not match up with the problems you're having here, or at least the practices you claim to have appropriated from these times do not transfer to the problems you're experiencing with Perl programming. I suggest you try a simpler approach to solve the problem at hand instead of introducing complexity you cannot handle to cater for potential problems later.