Multiple source values:
This is probably already obvious to you, but you can add multiple values in the drop down by clicking on the + button. So if you have values "US" and "United States" you can change both to "USA" with one flow step.
Multiple destination values for one-time batch campaign:
If you are producing a one-time campaign for this cleanup, you may find updating values in Excel and then loading the list to be easier. After about ten flow steps, the possibility of errors goes up as the performance slows down.
Multiple destination values for recurring campaign:
If you plan to update these values on a recurring basis, you should split up the 125 countries into smaller campaigns. Consider separating by region or something intuitive, as the name of the campaign will help in troubleshooting should a problem arise.