The sentence starts with "India has been a land" and ends with "than the warrior or the administrator." The middle segments must describe India's relationship with learning. Starting with Q, "of learning through the ages," defines the land. Then, S, "not indeed in the sense that education has been universal," clarifies the nature of learning. Next, R, "but in the sense that learning has always been very highly valued," contrasts with S. Finally, P, "and the learned man has been held in higher esteem," connects to the ending.
The order Q-S-R-P forms: "India has been a land of learning through the ages, not indeed in the sense that education has been universal, but in the sense that learning has always been very highly valued, and the learned man has been held in higher esteem than the warrior or the administrator."
Option 2 is correct.