Kotenseki kenkyū gaidansu: ōchō bungaku o yomu tame ni (Kasama shoin, 2012)
Part 1 of this text shows concrete examples of research in the fields of waka, monogatari, rekishi monogatari, diaries, essays (zuihitsu), and the performing arts. Part 2 concerns bibliography as the method that supports the readings given in Part 1 and provides simple explanations of how to handle primary sources, etc.

Nihon koten bungakushi no kiso chishiki (Yūhikaku, 1975)
Explains various works, people, and themes in classical Japanese literature and identifies the issues in researching them. While there are a large number of entry level materials and handbooks, I recommend this older work along with the one above. It is out of print but can easily be acquired from used booksellers.

Tokyo daigaku kyōyō gakubu kokubun kanbungakubukai, ed., Koten nihongo no sekai: kanji ga tsukuru nihon (Tokyo University Press, 2007)
Often the phrase “kobun” (古文) refers to works written in kana such as Tale of Genji and The Pillow Book, but this work examines Man’yōshū, Zeami, Rai San’yō, Natsume Soseki and others from various perspectives concerning sinographs and literary Sinitic, which it takes as their origin. The second volume of this work was published in 2011.

Genji monogatari to Murasaki Shikibu: kenkyū no kiseki. Kenkyūshi (Kadokawa gakugei shuppan, 2008)
Genji monogatari to Murasaki Shikibu: kenkyū no kiseki. shiryō (Kadokawa gakugei shuppan, 2008)
These texts contain the most important theories related to Tale of Genji and Murasaki Shikibu. Each essay has a explanatory section that explains its significance which aids in understanding. Another work in the same style is the four-volume Tēma de yomu genji monogatari ron (Benseisha, 2008-2010) which I also recommend.

Ikeda Kikan, Tosa nikki no hihanteki shochi ni kan suru kenkyū 1-3 (Iwanami shoten, 1941)
Using Tosa nikki as an example, this book begins by noting the distinction between an “original text” and its “original format,” the develops a case study of original text comparison in classical works by employing a large number of manuscripts. It also closely examines the causes of copying errors in detail. The more simplified Kotengaku nyūmon (Iwanami bunko, 1991) is by the same author.

Komatsu Shigemi, Kana: sono seiritsu to hensen (Iwanami shinsho, 1968)
This work explains in great detail the establishment of “kana” through the development from sinographs to man’yōgana, sōgana, and hiragana. For more specialized books on the subject, Ōbunsha has published the Komatsu shigemi chosakushū in thirty-three volumes along with other works he edited such as Nihon emaki taisei (Chūōkōronsha) and Nihon shoseki taikan (Kōdansha).

Katagiri Yōichi, Uta makura kotoba jiten zōteiban (Kasama shoin, 1999)
Gives precise explanation of words used in waka and place names and old ruins composed upon in waka. Many examples from waka are given, so it can be used not just as a dictionary and is enjoyable to learn from by reading through. The original was published by Kadokawa shōjiten in 1983.

Hirakawa Sukehiro, Āsa weirī: genji monogatari no hon’yakusha (Hakusuisha, 2008)
This is a biography of Arthur Waley (1889-1966), translator of The Tale of Genji, focusing on his translation work and his life. However, it provides in-depth analysis of word associations in Japanese and English and cultural background, and can be used for learning about the “words” of a literary work.