It looks like you're doing a lot of contortions and gymnastics to keep from developing a better process for getting things done. When you have to do that much work just to keep your pack-rat tendencies, you're really limiting your productivity. The trick is to overcome the things you do and like but that don't really help you. That sets apart the real pro from the amateur.

Someone already mentioned MANIFEST.SKIP, in which you can store regular expressions of things Makemaker or Module::Build should ignore. If you move your notes and snippets and whatnot to directories, you can just skip those directories and not worry about adding new files to them.

As for your question about $? and $!, you may want to read perlvar or my "Error Handling" chapter in Mastering Perl.

If you want to see how I make distros, you can read "Making New Distributions" from The Perl Journal. Basically, I cook a directory of TT templates.

Good luck :)