Hey Rob,
A couple of things...
I use the Delete Past Clipboard action to actively remove things I'm done with from the clipboard history.
I don't know if that will help with your task, but take note anyway – it's a useful feature.
It's possible to scrape URLs out of Mail with AppleScript – which might possibly streamline your workflow.
It's not always simple, so I'd need to see a sample or two.
P.M. me if necessary.
-Chris