Try out cleanth brook's book on writing and rhetoric. Also Jaques' Barzun's Simple and Direct. I assume your problem is expressing yourself clearly and effectively. Since you are a grad student, had you had problems with basic logic you would not have arrived where you are already.
EDIT: On the level of organizing thinking, these books will also help:
George Polya, How to Solve it Although it is about mathematics, I would recommend this book to anyone studying in university. It's a book about "thinking outside the box" if understood properly.
David Hackett Fischer, Historian's Fallacies. Studying the types of mistakes in informal reasoning is always instructive. This book is a good study of such errors in the field of history. I would also suggest checking out the various lists of argumentative/logical fallacies that can be found on the internet (I recommend the book because it is good).
Try out cleanth brook's book on writing and rhetoric. Also Jaques' Barzun's Simple and Direct. I assume your problem is expressing yourself clearly and effectively. Since you are a grad student, had you had problems with basic logic you would not have arrived where you are already.
EDIT: On the level of organizing thinking, these books will also help:
https://www.amazon.com/Simple-Direct-Jacques-Barzun/dp/0060937238