This is so much easier than it used to be. CiNii Books & Webcat Plus provide the readings for book and journal titles using katakana. The word division is also provided, so that can help you a lot with romanization. Checking for the book in Worldcat is also helpful because all Japanese titles have corresponding romanization using modified Hepburn in Worldcat.
For titles of articles 論題目 you will need to use your best guess. Usually the author provides an English translation in addition to the Japanese title. When you cite your articles, you need to (1) romanize the Japanese title, (2) provide the Japanese title, and (3) provide an English translation - do your own if one isn't provided. The English translation is for your non-Japanese readers.
The one thing you should not do is provide only an English title and say (in Japanese) because you leave your readers helpless in trying to get their hands on the item in question.
One of the problems that face all Japanese Studies researchers is how to read a Japanese name correctly. This problem is also faced by Japanese and they have resolved it in a number of ways - putting furigana beside their name, putting their name in English as well as Japanese, providing the reading for their name in the colophon of a book or the end of a journal article.
But what do you do if you need to request an article through interlibrary loan or romanize a name in a citation and you don't have access to those clues? You could try guessing (taking the 音読 or one of the possible readings), but that really isn't appropriate for a citation. If the person is a historical figure you will find the information in a 人名事典, but if we are talking about authors you might start with the National Diet Library's name authority records. This database will provide birth and death dates, pseudonyms, and other useful information to you.
There is also a database for