The PruneCruft thing was unfortunate. The purging of ~ files had gone in over my mild objections (I can't complain too much, I did the merge), and was then removed later when there were other objections that made me feel better about my own. It should be easy to add an "also" to PruneCruft (like except, but backward) or "patterns" to PruneFiles. I think someone has probably got a plugin to do what you want, but I'm not sure. #distzilla on irc.perl.org might know.
Files in bin/* don't strictly need a package declaration, but some things will expect them, like PodWeaver. You can just add the package -- which is what I do -- or you can change the FileFinders used by PodWeaver to only include :InstallModules and not :ExecFiles. #distzilla could also provide more step-by-step help, I think. I believe Marcel G. recently did just this change, so @MARCEL might have the change in it.
If PodVersion is finding =head1 VERSION that DZ added, it sounds like maybe you're using PodVersion -and- PodWeaver. The latter makes the former unnecessary.
Let me know if this is all unhelpful! ;)