However, you should write a comprehensive unit test suite against the code you currently have before changing anything, so that the new code can also be tested against those tests to ensure that it operates at minimum exactly the same way.

I just wanted to note that it's also possible to write the tests just against the command being run - luckily the interface to external commands is well-defined (usually just the commandline, STDOUT, and perhaps some files), so it's not too difficult to write a comprehensive test suite that tests the commands in the system or backticks, and then run that test suite against its pure-Perl replacement. Although I agree that a comprehensive test suite against the entire program would of course be very helpful and should eventually be built, the aforementioned approach allows one to make changes and write tests for a smaller scope first.