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. 

   When the Rambam mentions learning physics and metaphysics my feeling is that even though he says he is referring to how these subjects were understood in ancient Greece, I think you have to expand the definition to refer to Modern Physics and Metaphysics. But the later is harder to know. When the Rambam refers to Metaphysics that refers to the collected lectures in the book of Aristotle by that title. But nowadays I think you would have to include Kant and Leonard Nelson. Nelson started the new  Friesian-.SCHOOL; but even that needs modification as Bernays [one of his disciples] pointed out. 

[personally, I think it is a tragedy that Leonard Nelson is unknown.]

  Nelson was ignored, not from lack of quality, but from academic philosophy falling into the mud of analytic philosophy. They ignored real quality. 

  The fallacy of Analytic Philosophy is that analyzing language can not tell us anything about reality. It is hard to know smart people could fall into that. Analytic Philosophy is about as deep as a mud puddle. some people think that there are other approaches in philosophy after Kant that can replace Kant but i do not think that is right. 

I know there are people that think one ought to learn Torah alone, but that is more along the lines of the rishonim who held that way. But that is not the opinion of the Rambam or the Chovot Levavot.

[In Physics I suggest trying to get through every basic step from Newton until Einstein, Heisenberg, Feynman, and Susskind in the sense of "Bekiut" i.e. saying the words in order until you finish each book at least four times, and also listen to the lectures.

 my basic idea  about learning is different than that of universities in the USA. in the USA and the west in general there is an emphasis on finding what you are good at and have natural talent towards. and while i can see the justification in that approach, i have to say  that it does not seem very much geared towards the kind of goals that is have in mind in learning. to me there are things that one must learn whether he is talented or not. and there are things one must not learn whether talented or not.

 for example pseudo sciences like psychology, one must not learn even if they draw one in by their poison's sweetness. one the other hand there are things one must learn whether they appeal to one or not, like learning Torah. that is the old testament and the two talmuds with tosphot maharsha and the basic achronim like rav shach, rav isar meltzer, and the other gedolai Lita. plus two things the rambam emphasized--physics and metaphysics as you can see he mentions in the mishna torah and the guide. but since these are hard to understand i recommend the fast kind of learning  brought in the talmud--always one should be  גורס i.e. just say the words in order even if one forgets and even if one does not even know what one is saying.

I am sure my grandparents were relived that my dad was working on the  ultra secretive B-29in the USA rather than going over with the ground troops on D-Day. Even so I am sure their prayers for his safety never ceased until the end of the war. At least i can be proud that the B-29 Enola Gay is the airplane that ended the war. He remained in top secret  USA projects until around the 1970,s--like the U-2 and SDI  

''All who add to the mitzvot subtracts from them.'' ''כל המוסיף גורע''

 Even though there is some reason for a woman to wait seven  clean days, but that this depends on a  custom  brought in the Gemara that ''the daughters of Israel wait seven clean days even for a drop like a mustard seed'' is not really a good reason-- because to the Bach that means the color of mustard. A different reason would be like the  the Rambam that  straight nida blood [mentral cycle] and ziva [blood seen not at the regular time of seeing.]blood depend on an order of days that starts from the first time she sees blood-i.e. 7-11, 7--11,etc. But that  is not the way most Rishonim count the days. To most Rishonim each time a woman sees blood starts the start of day of nida. [That means the way to count is thus. Seeing blood on one day after a regular time since the last time is the start of days of nida. And days of nida are only seven days. If she see once or twice or the whole seven days makes no difference; she goes into a natural body of water the night after the seventh day. But if she sees on the eight day, that is a small zava-- i.e., she waits one day and goes into a natural body of water. If she sees again, that is still a small zava. But if she see three times during the 11 day  stretch of time after that seven starting time means she is a large zava and needs to count seven clean days.] And my general approach is that there is no reason to look for extra restrictions. If someone wants to be extra strict, that is fine. But they ought not make that seem like an obligation for everyone. [See the Ramban quoted in the Tur who counts the days in this way..] 

boys are made of snips, snails and puppy dog tails

For a man to call himself a woman can not change his molecular structure.  Since boys are made of snips, snails etc., while girls are made of sucrose and spice, that that DNA molecular structure can not be changed by calling it a different name. It would take a great deal of effort to turn a snail into sugar or spice. Even the basic elements are different.

reference: What are little boys made of?

What are little boys made of?
  Snips, snails
  And puppy-dogs' tails
That's what little boys are made of

What are little girls made of?
What are little girls made of?
  Sugar and spice
  And everything nice [or "all things nice"]
That's what little girls are made of

 A case of doubt about 4 or five damages (five oxen for one ox and five sheep for one sheep ) is an argument between the Rambam and the Raavad. The argument is if the owner of the injured ox has grabbed the ox that caused the damage. To the Rambam [laws of theft 2. law 12] he can keep what he grabbed, but the Raavad has several questions on that. It is more than what he damaged, and there is a doubt so no court that has authority to decide. The answer to the first question,  Rav Shach suggests that only half damages we say if he grabbed  he can keep [which is an open gemara- a person that grabs half damages can keep it until the court convenes and decides the case ], but in our case of four or five damages not. 

so rav shach seems to be saying that  in our case  of 4 or 5 times the damage would the raavad hold you take away the ox if it has been grabbed==even if not a doubt. only if it is a case of half damages that you do not take away the grabbed object. i mean to say that rav shach does not refer to the aspect that our case is one of doubt.  

For some reason, Rav Isar Meltzer did not suggest this answer, but rather refers this subject to an argument between the Rosh and Rabbainu Yona in Ketuboth pg 20. [paragraph 13 in the Rosh]-

Also he mentioned to look at the Rosh in Bava Kama 15 [paragraph 20 in the Rosh]. The Rosh brings there Rav Meir HaLevi who held תופס חצי נזק אין מוציאים מידו ( We do not take half damages away from one who grabs them) except for 1/2 damages-- which would work fine here for the Raavad except for the fact that the Raavad elsewhere in the Rambam holds we do not take half damages away from one who grabs them in general. So Isar Meltzer says the Raavad holds only in a case of doubt do we take away the  half damages because it is like a guarantee for a loan. and in the case of doubt for a guarantee for a loan we would hold  we do not take  away from one who grabs them. But here its is a ''kenas'' punishment for the damages, not monetary.