How to respond to peer review - a step by step guide to my first response?

Question

I'm in the process of responding to my first peer review (major revisions). There seems to be a lot of advice out there, (even some stuff here: How to write good Response Letters for the reviewers) but there are still a few etiquette and structural things I'm not sure about.

1. How do you structure your response? Do I respond to the comments chronologically in the order they appear in the paper, or do I create two separate sections for each reviewer? Maybe a "general" section, followed by separate comments for each reviewer?

2. Do I write a cover letter thanking the reviewers for their helpful comments?

3. How casual/formal should I be? Should I use contractions and a conversational (yet professional) style, or keep it as formal as the article itself?

4. Any dos/don'ts that would be helpful for me to know?

Answer 1

Variations are possible, but I have found that the following seems to be a fairly typically form of a response to reviewers:

• Begin with a letter to the handling editor and reviewers, in which you thank the reviewers for their useful feedback (even if it wasn't) and say you believe you've addressed all comments. If you've made any really major changes, a sentence or two here is a good to address them.
• Quote the reviews as sent and address each comment inline, either saying how you've done what they wanted or explaining why you haven't. I always organize by reviewer and address in the order of their comments (rather than the structure of the paper) because the goal is to clearly show that you have addressed all comments.

I recommend adopting a polite and semi-formal style. You can be a bit more informal than the paper, but I still don't use contractions.

Do not get argumentative with the reviewers, and do not blow off their criticisms. Even an apparently crazy criticism should be treated politely, and as a matter of confusion rather than as a personal attack.

Answer 2

I recommend the following. (Taken & modified from my answer here).

How to Respond to a Review
Every time I respond to reviewers, I create a document. I write a short paragraph thanking the reviewers for their time and state my responses to their comments are below. I copy each reviewer's comments, organized by reviewer (my preference). Beneath each comment, I write a response. If I make a change, I specify where and how I've updated the paper. If I disagree, I state that I respectfully disagree and then elaborate on why. I may choose to include tables, figures, or references in this document that are solely intended for the reviewers.

By doing this, each reviewer can quickly and easily see my responses to their comments as well as my responses to the other reviewers. Where there are similar or duplicate comments, I have similar or duplicate responses to make it easier for the reviewers. I have found this approach to work well---it also helps the editor weigh the totality of the review and my responses.

I send this PDF with the updated paper back in; my hope is that it demonstrates to the editor and reviewers that their comments have been taken seriously.

In terms of style, I prefer to write confidently, respectfully, in a semi-formal style. I explicitly address every comment, even if only by saying "changed", "complete", or "added two sentences to page 3, para 2 to clarify this.". When I disagree, I say so respectfully and provide a narrative to persuade and/or provide clear evidence as to why I take the position I do. I use bullets when it makes more sense to do so but I use them sparingly. I do not use a cover sheet. (Thank you to @Anyon for suggesting I add some style notes as well)

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Sample Format

Authors’ Response to Reviewer Comments
Manuscript: con575r1

We thank the reviewers for their time and helpful comments - their feedback substantially improved this paper. Our responses to each comment are provided below (reviewer comments are italicized in bold). The references listed at the end of this response are intended for all reviewers as cited in our responses.

Response to Reviewer 1...............p. X
Response to Reviewer 2...............p. Y
Response to Reviewer 3...............p. Z

Response to Reviewer 1
Comment 1 Text
Response: Response here to include any required evidence.

Comment 2 Text
Response: Response here.

Response to Reviewer 2
Comment 1 Text
Response: Response here to include any required evidence such as tables, figures, additional results, etc.

Comment 2 Text
Response: Response here.

References
Reference list (if needed) for anything in this Response Document that is solely for the reviewers & the editor. It is not just the references from the paper.