I have a Ph.D. in physics, and, needless to say, during the long and painful process of achieving it, I've definitely become more rational (in the broader sense) and a clearer thinker. My achievements may sound very basics to LW people, but you can consider them like the foundations of rationality, I guess.

• Calculus and Algebra taught me how to clearly apply the hypothesis->proof->thesis process. It might look a not so great achievement, but it is indeed, since it reflects in how I treat everyday issues (it's like the first step toward rationality in some sense)
• Programming courses taught me to break down complex processes in simpler atomic steps.
• Lab courses have taught me how to treat the data. Again this skill has been since then applied on a day by day basis
• General Relativity and Quantum Mechanics taught me that reality in not what it intuitively appears to be. This is a very important teaching: don't always trust your intuition, even if you really feel that you're right.
• Doing research activity, finally, taught me to calibrate my judgement (I used to be more often wrong than I expected), collect and elaborate data by myself and that apparently all the referees of Physical Review love to nitpick.