Is there a template for academic paper changes report?
At jakebeal's suggestion, I'm converting my comment from Jan. 12 to an answer:

Some people just use the referee's report and insert the information about what they did with each comment. So a minor comment (about fixing a typo for example) might be followed by just "Done." A comment about adding some more information might be followed by "Done; see page x, lines y to z." A comment that one didn't comply with might be followed by a careful explanation of the reasons for not complying. On the other hand, I've sometimes just written "I've complied with all the referee's comments except x. The reason for the exception is that ...."