One of the major points of the Gra that I think is important to emphasize is that every word of Torah weighs a much as all the other commandments.  Mainly that means the Old Testament the two Talmuds plus the Midrash. But in a certain sense it would include commentaries in so far as the commentaries   help in understanding even if they are not in fact part of the Oral and Written Law.

But this category of what explains the Law comes the Gemara itself according to the Rambam in  Laws of Learning Torah chapter 3 and that includes Physics and Metaphysics as he explains in the introduction of the Guide for the Perplexed.

I would to bring here the importance of a great book I have been looking at recently,-- the Even ha'Azel by Rav Isar Meltzer --a friend of Rav Shach. So when I say to get through the two Talmuds I mean with Tosphot [and Rashi when needed] Maharasha and the basic Litvak sages that bring to light very important aspects in the Gemara. [I do not mean just to run through it, except in the afternoon period which should be set aside for ''bekiut''. Fast learning is important as Rav Nahman of Breslov said in the Conversations of Rav Nahman 76 and which Rav Shick made a whole booklet out of. Fast learning is mentioned in the gemara Avoda Zara page 19.But that is for the afternoon period. The morning hours ought to go for preparation for the class of the Rosh Yeshiva your own study in the Avi Ezri, or the Hidushei HaRambam by Reb Haim of Brisk ]

i would like to mention here a subject i saw in the even haazel. let us say an ox gores a cow. there is paid 1/2 the ox and 1/2 the cow as it says somewhere in exodus. if the owner of the ox raises the value of the ox all the increase goes to him. but if the owner of the cow increased the value of the ox or it went upin value by itself, the tur writes the increase goes to him. but the rambam writes the owner of the cow gets only 1/2 damages from the cow even if it went up in value.  i have not written about this for a while because rav shach doe not bring up this issue and r. isar meltzer has a very long and difficult section on it which i am barely scratching the surface of. rav isar melzar says the reason for the rambam i that to r. akiva [whom we poskin like] the damaged person does not gain possession of the ox until after standing in court. this of course is a perfect answer however i seem to recall that rav shach said somewhere that the damaged person gains possession right away--but that might have been where he was explaining the raavad, so i am not sure if there is any difficulty, untili can recallwhat rav shach wrote.