I recommend the TextEdit Automator Action Pack by a company called Automated Workflows.
The downside is that it is not free but it's not too pricey. I think there
is a demo mode so you can at least check it out.
You're not able to enter your own regular expressions but the actions provided cover almost everything you need. I use the actions for every single Automator app I make which involves text files.
Alternatively, if you want to use your own regex commands you can install a scripting addition for AppleScript made by a company called Smile. It's called Satimage and it allows regular expressions to be used in AppleScript. Visit the Satimage dictionary for usage.
If you install that scripting addition then you can include any regular expression you want in Automator by including an AppleScript action and then pass variables back and forth, though I think the TextEdit Automator pack will be easier and more efficient.