I recommend the following course of action:

First, collect all the reviewer comments into a single Word document.  You may organize them in any way that seems reasonable, but I usually keep them organized by reviewer.  So, create a separate heading for each reviewer in the document.  I strongly suggest that you do this by cutting and pasting the exact text from the reviewer comments.

Next, edit the reviewer comments to keep only the exact text that needs to be addressed.

Reformat everything to get rid of bold, italics, underlining, and the like.

Title this document “Reviewer Response YYYY-MM-DD”.

Next:

1. Identify the changes in the statistical analysis that need to be  made first.  This is essentially an addendum to the Statistical Analysis Plan.

2. Identify the changes in the Discussion that need to be made.  Review  all of these changes in light of the changes in the Results that  may have occurred.

3. Identify the other types of changes (editing, wordsmithing, general carping or cavilling).

Now you are ready to re-run the statistical analysis having made the necessary changes in methodology.  Of course, you will keep this completely separate from your previous work, to ensure that you can always trace back your work.

Finally, you are ready to make changes in the manuscript.  Before starting this process, get your Reviewer Response document ready.

1. Make changes in the Results section as necessary.

2. Then, make changes in the Discussion section accordingly.  These can be done in parallel if that is easier, such as when you have many sub-sections in the Results.

3. Make changes in the Statistical Methods section as needed.

4. Make editorial changes that have been indicated.

As you make these changes, indicate in the Reviewer Response  document under each item what you have done to fix things.  I usually  format the reviewer comment in italics and my response as normal  text.  So an example would look like this:

Reviewer A:

p4 l5 You misspelled the word “thorough” as “through”.

This was corrected.

p6 l20 It is standard practice to include the p-value for this test.

The p-value for the test was included.  This was also changed  in the other sections of the manuscript.

If the reviewers identified some global or larger issues, you may want to break those out separately in an initial section.

Finally, write an introduction to the Reviewer Response.