As far as I understand it, in Perl you first need to create a new file with the desired output then rename that file to the original name. So in my case that would be with the rename function ... If there is a better way to get what I want, I'm open to suggestion.

You are on the right track. For some history and solutions to this fascinating and tricky problem see this old node Re-runnably editing a file in place, especially its "See Also" section.