[NoboruWataya]

What do you mean exactly, are you just looking for software that will highlight the differences between two documents? That software exists already.

[nashashmi]

Yes that software does exist and currently my go to method (convert pdf to word document, compare changes in word).

The ideal system would highlight (sets of) text that that's common between both documents and underline text that is original. Or vice versa.

[freejazz]

You can run redlines of PDFs in Adobe Acrobat pro, no need to conver to word.

"The ideal system would highlight (sets of) text that that's common between both documents and underline text that is original. Or vice versa."

Just change your settings in microsoft word.