The essence of learning Torah for its own sake
We normally understand the phrase "to study Torah for its own sake" (and the Jewish tradition emphasizes the importance of precisely such study) as study without practical purpose, study for the sake of studying. Rav Kook casts the phrase in a new light, meaning "to study Torah for the sake of Torah," that is, for its ability to renew and deepen the individual who studies it. This involves the study of the interconnections between all of the details and specifics of the commandments and the general ideological and philosophical principles. Such study, as demonstrated in the preceding paragraph, is necessary in order to help our generation reach a state of teshuvah.
An additional note on the connections between Paragraphs 1, 2, and 3
Just as the "kosher" alone is insufficient and must be raised to a higher level of idealism and sanctity, so, too, the "usual" study of Torah as no more than a collection of laws is inadequate (especially as this was the type of study that led to its rejection by an enlightened generation). Study of Torah must include the revelation of the meaning of its laws and their connection with general values. This is the message of paragraph 3.