Ah, Shirou, you can call me Light. There are some rather major facts being omitted leaving you in the dark, by your father, your friends, and my colleagues. Of course, I will respect your friends and my colleagues on some of this, but not on all of it. I most certainly won't respect your father refraining from properly teaching you the nature of reality, presumably hoping that you will give up on your dream to become a hero due to incompetence. To rectify that, I will offer a general primer that you should check out with Rin Tohsaka, if you can.
Quite simply, as far as you should be concerned, the Science vs Magic trope is in full effect. The stronger the science, the weaker the magic, and vice versa, at least generally. Miracles are, quite simply, what is impossible through science, and they stop being so the moment that they are possible through science.
At the moment, there are five major miracles, also known as True Magic. I only know of four of them, and only three of those four with any comprehensive overview. The first true magic is known as denial of nothingness, and beyond that, I guess that it is the miracle of creating something real and permanent, from nothing. The second True Magic is based on the operation of parallel worlds, also called the Kaleidoscope, which has various applications, such as accessing an infinite amount of magic energy. The third True Magic is called Heaven's Feel, and it is the ability to affect the soul beyond any Magecraft. It can be used to make someone immortal, turning their soul into a perpetual motion machine, and making them immune to any attack that doesn't affect the soul. The Fourth True Magic is unknown. The reasons for this are unknown. The Fifth True Magic is an esoteric form of Time Manipulation that can perform resurrections, at the small, small cost of massively increasing the universe's entropy. It can also do things like give the user the ability to overlap themselves into a single moment, attacking numerous times at the same time. Of those True Magic, you might encounter the Second and Third True Magic, as those are heavily entwined with the Holy Grail War, and of those two, I estimate you will be more likely to encounter the Second True Magic than the Third.
As for your personal magecraft, you can develop a reality marble, what the original Emiya Archer may have, due to how mentally twisted you are, as that is a requirement to gain a reality marble. I would recommend avoiding trying to project your reality marble on the outside world without significant preparations at the moment, as you will most likely only waste your energy. Instead, you should try to draw a mundane knife, or possibly preferably, mundane sword, from yourself, after practicing a variety of other Magecraft to get a decent grasp of what you are doing. Of course, do this only under someone else more competent than you.
Additionally, you are an idiot. You don't need to make Magic Circuits to use Magecraft, and that pain of feeling a hot iron rod inserted into your spine actually signifies how insanely close you are to dying, each time you do so. Get either Rin Tohsaka or Chloe to help you out here, Rin Tohsaka wouldn't notice this in the first place if you didn't straight-up tell her as, in her words, she always messes up on what is really important. Of course, given that your father, Kiritsugu, didn't catch this mistake, you shouldn't hold it against Rin, she's only a supposed genius Magus.
As for another way to improve your Magecraft, your "Elemental Affinity" is the unusual Element of Sword. Elemental Affinities extend a bit conceptually, such that a standard Fire Elemental Affinity can be used to control heat, and then be used to attack with Ice, and a standard Earth Elemental Affinity extends conceptually with "cultivation of energy" and similar, earthy, things, so feel free to think a little outside the box with your Elemental Affinity once you get more experienced. For reference, Rin Tohsaka is called an "Average One", as she is a freak of nature that has the five elemental affinities of Fire, Water, Earth, Wind, and Ether. Further down conceptually, Ether is, quite simply, Magic Energy. Additionally, it should be noted that Magic Energy can be divided into categories, with Od being magical energy from within yourself, Mana being magical energy from the environment, and Prana being the combination of both Od and Mana. Od can be increased through physical health, so good job on being a brute, but it is worthless without Magic Circuits, or equivalents, outside of circumstances that are irrelevant to you at the moment, such as the likes of years of martial arts training having the potential to grant minor abilities.
It is also worth noting that there is this thing called an "Origin" that is extremely relevant to you, however, if you know of it, it becomes an irresistible compulsion. It grants a minor boost to your abilities whenever you act in conjunction with your origin, as well as a minor boost to your magecraft if it relates to your origin. I think you can live with it, but I won't tell you it without your explicit permission. For reference, your father, Kiritsugu, had the origin of Binding and Severing, which allowed him to make bullets out of his ribs that caused necrosis in human flesh, destroyed magic circuits, and completely countered conventional magecraft. He also may have found that anything he tried to repair got similarly binded and severed instead, and his social life may have been impacted by this as well, since it seems like he simply "bound" people to him and "severed" his relationships with them, usually ending in their death.
As one last note, remember the Fuyuki Fire? That was caused by the last Holy Grail War, the one your father participated in. The Holy Grail is currently tainted, however, I am not sure that it wasn't tainted from the start. I suspect that a certain source of Cursed Gold was integrated into the Holy Grail, causing the first three Holy Grail Wars to not have any victor, even before it was extremely corrupted by Angra Mainyu. It does make a fair amount of sense.
You will be participating in the Sixth Holy Grail War, and Kiritsugu participated in the Fifth Holy Grail War. I would recommend you avoid killing any Servants, except for Gilgamesh and only if he is not a child (Child, not Teenager), as that will give the Holy Grail more fuel to cause destruction. There are other things I should say, one detail in particular relating to the ending of the Fifth Holy Grail War, but you have to promise not to rush in and get yourself killed first, as that won't save anyone. It also wouldn't be particularly entertaining.
