Your build tool should be able to be told to copy certain files and where to put them, so you just need to figure out how to do that. What are you using? Dist::Zilla?

Update - oh I see, Minilla. Looks cool, never used it. It might not do what you need based on this,

Minilla sets install script files as ['script/*', 'bin/*'] by default.

(Note. This option doesn't affect anything if you are using ModuleBuildTiny or ExtUtilsMakeMaker, for now. If you are using ModuleBuildTiny, you MUST put scripts in script/ directory.)

If it's true it can't handle your use case, there might be a way to do as a pre-step. But really, I think you already recognize the fact that you should figure out the root issue - don't use .pl when it should be .pm.