Q: How can I deal with conflicting editor and reviewer comments?
I received a final decision not included in your mentioned final Editor decisions: "I have declined it for publication at this time...but with additional work, you may be able to turn this into a more suitable paper." Furthermore, the reviewer comments were very confusing: they seem to have read the manuscript only partially. Additionally, the main suggestion provided by the editor (modeling is weak, and should be removed) contradicts the reviewer suggestion (modeling must be improved). Do you have any suggestion on how I can deal with the conflicting comments? Should I follow the editor's suggestion or the reviewer's?
It is not unusual to have conflicting reviewer comments. In such cases, you have to take a call on whether you agree with the reviewer’s opinion or the editor’s. You should follow the comment that you agree with. If you feel you can improve the modeling substantially, you should do so. However, if you are not sure how to improve the modeling, you can consider deleting it.
Whatever your decision, you should provide a point-by-point response to each of the comments, both the reviewer’s and editor’s. If you decide not to follow a comment, you should accordingly give a detailed and well-reasoned explanation. Additionally, in the covering letter to the editor, explain that you had to choose between some of the comments as they were conflicting, but you have provided reasons for your choice.