Well, you might be right, but if the only tool you have is a hammer, you better start thinking everything looks like a nail.
I wouldn't dismiss the macro approach out of hand, becuase most likely you will be turning a text file with a list of 5,000 file paths into a series of commands (using regex) that apply your regexes.
This looks like it may help you apply multiple regexes to each file:
I can't find a plugin to run commands against multiple files, but this will help you open and save them:
You also might want to look at other tools (perhaps sed) which are designed to do what you're talking about.