You don't need to clip whole article to find the text you wanted. Just copy the text, then hit "Ctrl+Alt+V". This makes a new note in Evernote with the selected text. (It actually copies whatever is in your clipboard, so if you have a smarter clipboard function it may be made more automatic). You could then combine these texts under a new note. The notes seem to retain the links that they were captured from, essentially the clipping you were doing.
On Windows there is a neat shortcut for this type of use case. Say you are reading any content on the web, or local copy of PDF. Just highlight the text with your cursor and Copy or "Ctrl + C", then hit "Ctrl + Alt + V". This opens up a new note in Evernote, and pastes this content. These new notes are automatically given the title "Untitled Note" which you can make a search shortcut "intitle:"Untitled Note" to easily find them. You can then select all these notes and merge under whichever paper you were reading. Note that this requires Evernote to be running in background. I have found this trick way too late as I was also looking for a similar use (I'm an academic too). It is cool that Evernote has nuggets like this.