it reports that it is in use by another program

Process Explorer from Microsoft SysInternals is your friend. It allows for searching for what processes/DLLs have a file open (Ctrl+F, enter the search string), and for executables shows the hierarchy of comands. For example, when I run perl from Notepad++'s NppExec plugin, so it's in a little command shell, it shows the notepad++.exe > perl.exe call-chain: https://i.imgur.com/3CczLaH.png

how can I 'stop' usr/perl/bin so I can delete it?

you can kill any perl.exe using Task Manager or Process Explorer. If you're trying to stop the process that has a file or folder open, after searching in Process Explorer, it will tell you the PID of the process that has it open, so you can use Process Explorer or Task Manager to kill the process that's holding it open.

edit:

I never get any notifications to the email address

Notifications go to your PerlMonks Message Inbox, not to your email. Perlmonks was designed to not send any email (except maybe a welcome email -- I don't remember for sure -- and your plaintext password when you request a password reset).