Copy/paste through Putty is cake. Anytime you highlight something in Putty, it's automatically "copied". Show your config, highlight the ACL and paste it into notepad. To paste, just right-click.
I seem to recall that, in later versions of the IOS you can edit your ACL and add or remove lines dynamically without wiping it out and starting over like you used to have to do. I've never done it (don't get my hands on many Ciscos nowadays), but it's there.
- G